Brucella phage polynucleotides and uses thereof

ABSTRACT

An isolated polynucleotide is disclosed which comprises a nucleic acid sequence of a  Brucella  phage, the nucleic acid sequence being specific to the  Brucella  phage and comprising a sequence selected from the group consisting of SEQ ID NOs: 387-393. An exemplary polynucleotide sequence is one which comprises at least 100 consecutive nucleotides of a nucleic acid sequence as set forth in SEQ ID NO: 396. Uses of such sequences are further disclosed.

RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No. 13/500,360 filed on Apr. 5, 2012, which is a National Phase of PCT Patent Application No. PCT/IL2010/000812 having International filing date of Oct. 7, 2010, which claims the benefit of priority of U.S. Provisional Patent Application No. 61/272,574 filed on Oct. 7, 2009. The contents of the above applications are all incorporated herein by reference.

SEQUENCE LISTING STATEMENT

The ASCII file, entitled 59350SequenceListing.txt, created on May 5, 2014, comprising 409,600 bytes, submitted concurrently with the filing of this application is incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates to Brucella phage nucleic acid sequences and uses thereof.

Brucella are Gram negative, small coccobacilli bacteria. They are animal pathogens causing abortions in the natural hosts, in the latest period of pregnancy. Genus Brucella includes 10 species divided to smooth and rough outer membrane LPS bearing organisms. Three smooth Brucella species, (B. melitensis, B. abortus and B. suis) associated with small ruminant, bovid and swine brucellosis, respectively, are zoonotic to humans. Less frequently, B. ceti and B. pinnipedialis associated with marine mammal brucellosis have been documented as causative agents of human brucellosis. In addition, B. canis that is associated with canine brucellosis is a rough organism that causes human infection. The disease in humans is presented as undulant fever also known as Malta fever, and it may sequel to a chronic disease or manifestation of meningitis, osteomyelitis, endocarditis and other complications. In rare occasions the disease may become fatal.

Brucella phages are bacterial viruses specific to Brucella species. A review of Brucella phages and their taxonomical relatedness was published in 1981. All contemporarily known Brucella phages were shown to comprise a similar icosahedral head and short tail morphology belonging to the family Podoviradae. The studied phages were shown to be closely related according to antigenic and physiological properties and resistance to chemical and physical agents. These findings have led the authors to include the summarized variants within a single species and propose phage Tb as type virus (Ackerman, H.-W., Simon, F., and Verger, J.-M. 1981. Intervirology 16: 1-7).

Brucella phages have linear double stranded DNA in size around 38 kilo base pairs. Restriction enzyme digestion analyses of phages Tb, Fi, Wb, Iz and R/C have shown similarity amongst the DNAs and little evidence has been found for lysogenic existence of the phages or presence of plasmid forms in the hosts.

Previous studies have established guanosine-cytosine content of 45.3-46.7% in phage Tb whereas a higher percentage of 48.9% was anticipated in other phages.

Use of phages as therapeutic agents of a pathogenic disease has been indicated by several researchers (Brüssow, H. 2005. Microbiol. 151: 2133-2140; Summers, W. C. 2001. Ann. Rev. Microbiol. 55: 437-451).

In addition, Brucella phages have been employed in Brucella typing and a phage susceptibility test has become instrumental in classification and establishing a taxonomical tree of genus Brucella. Specifically, it was suggested that division of genus Brucella into nomen-species is partly justified according to their species specific phage susceptibilities that also correlated well with host affiliation of the strains. Brucella phages have been divided into 7 groups according to their infectivity to Brucella spp. Phage Izatnagar (Iz₁) represents group 6 that is infective to all smooth Brucella nomenspecies and partly to rough strains (Corbel and Tolari, 1988, Res Vet Sci; 44: 45-49).

-   Zhu et al., 2009 [Int. J. Mol. Sci. 10: 2999-3011] teaches a partial     sequence for the Tb (Tbilisi) Brucella phage. -   Rigby et al., 1989 [Can J Vet Res. 53: 319-325] teaches a partial     sequence for Nepean phage and other lytic phages of Brucella     species. -   U.S. Patent No. 20030017449 teaches detection of Brucella using     Brucella phage.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence of a Brucella phage, the nucleic acid sequence being specific to the Brucella phage and comprising a sequence selected from the group consisting of SEQ ID NOs: 396 and 387-393.

According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide being at least 15 nucleotides in length which hybridizes to the isolated polynucleotide of the present invention.

According to an aspect of some embodiments of the present invention there is provided a method of down-regulating expression of a gene of interest in a bacteria, the method comprising transforming bacteria with a nucleic acid construct which comprises a Brucella phage regulatory sequence, thereby down-regulating expression of the gene of interest.

According to an aspect of some embodiments of the present invention there is provided a nucleic acid construct comprising at least 100 nucleotides of a nucleic acid sequence as set forth in SEQ ID NO: 396.

According to an aspect of some embodiments of the present invention there is provided a nucleic acid construct comprising:

i. a polynucleotide encoding a gene of interest operationally fused to a Brucella promoter;

ii. a first Brucella phage sequence fused to a 5′ end of the promoter, the first sequence comprising at least 100 nucleotides of a nucleic acid sequence as set forth in SEQ ID NO: 394; and

iii. a second Brucella phage sequence fused to a 3′ end of the gene of interest, the second sequence comprising at least 100 nucleotides of a nucleic acid sequence as set forth in SEQ ID NO: 395.

According to an aspect of some embodiments of the present invention there is provided a recombinant Brucella phage which identifies Brucella bacteria by outputting a detectable signal.

According to an aspect of some embodiments of the present invention there is provided an isolated Brucella bacterial cell comprising the recombinant Brucella phage of the present invention.

According to an aspect of some embodiments of the present invention there is provided a method of diagnosing a Brucella infection in a subject, the method comprising contacting a sample of the subject with the recombinant Brucella phage of the present invention, thereby diagnosing the Brucella infection.

According to an aspect of some embodiments of the present invention there is provided a method of diagnosing a Brucella infection in a subject, the method comprising contacting a sample of the subject with the isolated Brucella bacterial cells of the present invention, thereby diagnosing the Brucella infection.

According to some embodiments of the invention, the isolated polynucleotide comprises at least 100 consecutive nucleotides of a nucleic acid sequence as set forth in SEQ ID NO: 396.

According to some embodiments of the invention, the isolated polynucleotide comprises the sequence as set forth in SEQ ID NO: 396.

According to some embodiments of the invention, the isolated polynucleotide comprises a nucleic acid sequence as set forth in SEQ ID NOs: 387-393.

According to some embodiments of the invention, the isolated polynucleotide has the nucleic acid sequence as set forth in SEQ ID NO: 1.

According to some embodiments of the invention, the isolated polynucleotide comprises at least one nucleic acid sequence being selected from the group consisting of SEQ ID NO: 394 and 395 in a forward or reverse orientation.

According to some embodiments of the invention, the isolated polynucleotide further comprises a heterologous nucleic acid sequence and a heterologous promoter sequence which directs expression of the heterologous nucleic acid sequence.

According to some embodiments of the invention, the nucleic acid sequence comprises a transcriptional regulatory region.

According to some embodiments of the invention, the transcriptional regulatory region comprises a brucella phage promoter.

According to some embodiments of the invention, the isolate polynucleotide comprises a sequence as set forth in SEQ ID NOs: 2-386.

According to some embodiments of the invention, the heterologous nucleic acid sequence encodes a detectable moiety.

According to some embodiments of the invention, the heterologous nucleic acid sequence encodes a polypeptide which is lethal to Brucella.

According to some embodiments of the invention, the bacteria comprises Brucella bacteria.

According to some embodiments of the invention, a strain of the Brucella bacteria comprises B. Suis or B. melitensis.

According to some embodiments of the invention, the gene is endogenous to the bacteria.

According to some embodiments of the invention, the gene is endogenous to a phage of the bacteria.

According to some embodiments of the invention, the regulatory sequence comprises at least 100 nucleotides of a nucleic acid sequence as set forth in SEQ ID NO: 396.

According to some embodiments of the invention, the regulatory sequence comprises the sequence as set forth in SEQ ID NO: 396.

According to some embodiments of the invention, the regulatory sequence further comprises the sequence as set forth in SEQ ID NO: 397.

According to some embodiments of the invention, the regulatory sequence is flanked by a transposon sequence.

According to some embodiments of the invention, the nucleic acid construct comprises a nucleic acid sequence as set forth in SEQ ID NO: 396.

According to some embodiments of the invention, the nucleic acid sequence is flanked by a transposon sequence.

According to some embodiments of the invention, the gene of interest encodes a therapeutic polypeptide.

According to some embodiments of the invention, the gene of interest encodes a detectable moiety.

According to some embodiments of the invention, the gene of interest is comprised in a Lux operon.

According to some embodiments of the invention, the detectable signal is a luminescent signal.

According to some embodiments of the invention, the recombinant Brucella phage comprise lytic activity.

According to some embodiments of the invention, a genome of the phage comprises a polynucleotide sequence which encodes the detectable signal.

Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 shows read sequences that corroborate on the specific consensus largest contigue of 38255 nucleotides identified by the sequencing machine. It can be seen that C and A are each distributed equally in 8 contigues at nucleotides 5549 and 5550 leaving a gap of a single nucleotide in one or the other position. This indicates an SNP (or heterozygote) in position 5549 between C and A, respectively. In each construct, N is correctly identified as C.

FIG. 2 depicts 9 phage Iz₁ DNA fragments that have been successfully sub-cloned into plasmid pBS. These fragments hybridized with whole Phage Iz₁ genomic DNA and nucleotide sequencing confirmed their accurate sequence that was identical to the overlapping sequences in the complete phage genome.

FIGS. 3A-B are schematic diagrams illustrating two plasmid constructs based on Brucella plasmid pBBR1mcs-4.1-II1053Lux_(CDABE). The constructs include Phage Iz₁ DNA fragments that extend between nucleotides 15500 to 16509 and 18579 to 19630 and one of Tn5 mosaic ends added in the correct orientation to their 3′ and 5′ ends. These engineered fragments were cloned up- and downstream of Lux, respectively, in two orientations.

FIG. 4 is a schematic diagram illustrating the position of the primers used to construct the plasmid constructs depicted in FIG. 3B.

FIG. 5 is a flow diagram illustrating the steps taken to generate a Brucella phage carrier clone.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates to Brucella phage nucleic acid sequences and uses thereof.

Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not necessarily limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways.

The Brucella species are important zoonotic pathogens affecting a wide variety of mammals. In agriculturally important domestic animals, these bacteria cause abortion and infertility, and they are of serious economic concern worldwide. Brucella species that infect humans cause an undulating fever, which if untreated, can manifest as orchitis, osteoarthritis, spondylitis, endocarditis, and neurological disorders. In rare events it may be fatal.

The present inventors have sequenced the entire genome (38,254 base pairs) of the Brucella phage Iz₁ as a genotype representative of all other Brucella phages. Two genomic Brucella phage Iz₁ populations were identified, differing between C or A at nucleotide 5549. BLAST analysis of this sequence revealed 6 regions of homology with Ochrobactrum anthropi ATCC 49188 chromosome 1—see Table 2 in the Examples section herein below. Subtraction of these sequences from the sequence of the full length genome, leads the inventors to the discovery of novel polynucleotide sequences which are specific to Brucella phage (e.g. SEQ ID NOs: 387-393).

The information gleaned from the sequence has allowed the inventors to identify apparent sequence of minimal presence of ORFs, which can be used for inserting genes of interest (for example, those encoding detectable moieties) into the phage, without affecting its lytic activity. Thus, development of a recombinant Brucella phage has been sought based on recombinational replacement of this site in the phage genome with a detectable signal (e.g. Lux operon). Due to the outputting of this signal, such a phage could be used to identify Brucella bacteria. Phage carrier Brucella clones were generated in which phage Iz₁ coresided in the cells in presence of plasmid pBBR1mcs4.1-II1053/lux_(CDABE)/15B-18B (FIG. 3B), providing unlimited opportunities for recombinantional events to occur between the Lux operon on the plasmid DNA and the Brucella phage DNA.

In addition, the present inventors have identified regulatory regions in the phage which possess regulatory function and were shown to be capable of down-regulating light expression endowed by the plasmid indicating potential implementation of such a gene regulation mechanism within Brucella bacteria.

Thus, for example, the present inventors identified a fragment of phage DNA which can down-regulate a gene operatively linked thereto (SEQ ID NO: 396; 19630-18579) following transformation into Brucella bacteria. When this sequence was transformed into Brucella bacteria, together with an additional phage DNA fragment (SEQ ID NO: 397; 16509-15500), it conferred different lethal activities on Brucella species, being the most lethal to lethal to the B. abortus strain 544, less severely lethal to B. melitensis and non-lethal to the B. suis strain of Brucella. Correspondingly, the down-regulatory activity of this fragment was also shown to be species specific.

Knowledge of phage regulatory regions should add to computational identification of additional unrecognized regulatory sequences within the genome of Brucella. This approach has already been demonstrated in the legume endosymbiont Sinorhizobium meliloti (del Val C, et al., Mol Microbiol 2007; 66: 1080-1091), that is belonging to the alpha-proteobacteria class, as also Agrobactrum tumefaciens, the causative agent of crown-gall disease in plants and Brucella, indicating close relatedness and therefore possible shared functions between these organisms (Inon de Iannino N, et al., J Bacteriol 1998; 180: 4392-4400).

Thus, according to one aspect of the present invention, there is provided an isolated polynucleotide comprising a nucleic acid sequence of a Brucella phage, the nucleic acid sequence being specific to the Brucella phage and comprising a sequence selected from the group consisting of SEQ ID NOs: 387-393.

As used herein, the term “phage” (synonymous with the term “bacteriophage” refers to a virus that selectively infects prokaryotes—such as bacteria. Many bacteriophages are specific to a particular genus or species or strain of cell.

The phage is typically a lytic bacteriophage.

A lytic bacteriophage is one that follows the lytic pathway through completion of the lytic cycle, rather than entering the lysogenic pathway. A lytic bacteriophage undergoes viral replication leading to lysis of the cell membrane, destruction of the cell, and release of progeny bacteriophage particles capable of infecting other cells.

A lysogenic bacteriophage is one capable of entering the lysogenic pathway, in which the bacteriophage becomes a dormant, passive part of the cell's genome through prior to completion of its lytic cycle.

According to one embodiment, the phage is a Tb type phage, for example Phage Iz₁.

A sequence specific to a Brucella phage is one which is present in the phage and not present in other organisms—i.e. unique to Brucella. Since the sequence of the Brucella phage genome is now known, Brucella phage specific sequences may be identified using BLAST or other similar programs.

According to one embodiment, the Brucella phage specific sequence does not comprise more than 70% identity with another nucleic acid sequence as verified using a sequence alignment software such as BLAST analysis.

According to one embodiment, the Brucella phage specific sequence does not comprise more than 60% identity with another nucleic acid sequence as verified using a sequence alignment software such as BLAST analysis.

As used herein the phrase “an isolated polynucleotide” refers to a single or double stranded nucleic acid sequences which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).

As used herein the phrase “complementary polynucleotide sequence” refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers to a sequence, which is at least partially complementary and at least partially genomic. A composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. Such intronic sequences may further include cis acting expression regulatory elements.

According to one embodiment, the isolated polynucleotide comprises at least 15, at least 20, at least 40, at least 50, at least 100, at least 200, at least 500 or at least 1000 consecutive nucleotides of the sequences as set forth in SEQ ID NOs: 387-393.

Thus, the polynucleotides of the present invention may be from 15-38,254 nucleotides long.

It will be appreciated that homologues of the sequences described hereinabove are also envisaged by the present invention. Accordingly, the polynucleotides of this aspect of the present invention may have a nucleic acid sequence at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 87%, at least 89%, at least 90% at least 91%, at least 93%, at least 95% or more say 100% identical to the sequences derived from SEQ ID NOs: 387-393, as determined using BlastN software of the National Center of Biotechnology Information (NCBI) using default parameters.

Thus, the present invention encompasses nucleic acid sequences described hereinabove; fragments thereof, sequences hybridizable therewith, sequences in the opposite orientation thereto, sequences homologous thereto, sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or man induced, either randomly or in a targeted fashion.

Exemplary polynucleotides contemplated by the present invention are those that comprise the nucleic acid sequence as set forth in SEQ ID NOs: 1 and 387-393.

Other exemplary polynucleotides contemplated by the present invention are those that comprise regulatory regions within the sequences as set forth in SEQ ID NOs: 387-393, such as at least 100 consecutive nucleotides of the regulatory region as set forth in SEQ ID NO: 395 shown by the present inventors to possess down-regulating activity of a gene operationally linked thereto, when inserted in the opposite orientation (i.e. SEQ ID NO: 396). Another regulatory sequence includes SEQ ID NO: 394, both in the forward or reverse orientation. This is also present in the complete phage genome possibly affecting regulatory functions of phage Iz₁ genes.

Using bioinformatic tools, the present inventors identified additional regulatory regions within the full length sequence of the phage genome which may serve as promoter sequences (i.e. transcriptional regulatory regions) in the phage (SEQ ID NOs: 2-386). Such promoter sequences may be placed upstream of a heterologous nucleic acid sequence so as to promote transcription thereof. Moreover, the downregulatory activity might be used to identify important chemicals that change the activity of the transcriptional regulatory regions, thereby facilitating development of novel drugs.

Other sequences which encode putative polypeptides are also provided and also considered to be in the realm of the present invention. Such sequences are provided in Table 1 herein below. Polynucleotide sequences encoding such polypeptides may be used for various purposes. Thus, for instance a polynucleotide sequence encoding a putative lysin or holin may be used to selectively kill Brucella cells. The advantages of lysin-based therapy are numerous: they can be prepared with high purity and possess high specific activity; they exhibit rapid lethal action; they are nontoxic; and apparently, antibodies that form against these proteins do not neutralize their lytic activity. Lastly, no bacterial resistance develops to these proteins, probably because they possess multiple domains for cell wall binding and hydrolysis.

Examples of additional important polypeptides are:

1. Secretory proteins including flagellar proteins (secretion Type III, This apparatus is related to the injectisome used by many gram-negative pathogens and symbionts to transfer effector proteins into host cells) and VirB (Type IV, The translocation of DNA across biological membranes is an essential process for many living organisms. In bacteria, type IV secretion systems (T4SS) are used to deliver DNA as well as protein substrates from donor to target cells. The T4SS are structurally complex machines assembled from a dozen or more membrane proteins in response to environmental signals The translocation of DNA across biological membranes is an essential process for many living organisms. In bacteria, type IV secretion systems (T4SS) are used to deliver DNA as well as protein substrates from donor to target cells. The T4SS are structurally complex machines assembled from a dozen or more membrane proteins in response to environmental signals)

2. Phage integrase—catalyses the site specific integration and excision of the bacteriophage in the lysogenic cycle.

3. Toxins, phospholipase—degrade phospholipids, protease—degrade proteins.

TABLE 1 % alignment Mis gap q. Subject id Description identity length matches openings start q. end ref|YP_672794.1| hypothetical protein 52.46 812 347 13 37128 34810 Meso_0225 [Mesorhizobium sp. BNC1] ref|YP_672803.1| hypothetical protein 47.39 652 336 11 29673 27739 Meso_0234 [Mesorhizobium sp. BNC1] ref|YP_672798.1| hypothetical protein 79.76 336 68 0 32487 31480 Meso_0229 [Mesorhizobium sp. BNC1] ref|NP_102255.1| hypothetical protein 35.80 810 501 16 37143 34771 mll0462 [Mesorhizobium loti MAFF303099] ref|ZP_06361176.1| conserved hypothetical 36.76 759 443 13 37074 34909 protein [Rhodopseudomonas palustris DX-1] ref|YP_672806.1| hypothetical protein 69.35 323 97 2 27275 26313 Meso_0237 [Mesorhizobium sp. BNC1] ref|YP_224275.1| hypothetical protein 33.16 781 474 17 5921 8119 LPPPVgp44 [Listonella phage phiHSIC] ref|YP_672793.1| phage uncharacterized 58.62 348 136 10 1378 359 protein [Mesorhizobium sp. BNC1] ref|YP_672793.1| phage uncharacterized 35.58 104 63 3 2737 2438 protein [Mesorhizobium sp. BNC1] ref|YP_224270.1| putative helicase 41.36 515 280 6 12291 13769 [Listonella phage phiHSIC] ref|YP_224270.1| putative helicase 52.63 76 36 0 12089 12316 [Listonella phage phiHSIC] ref|YP_224270.1| putative helicase 63.33 30 11 0 11996 12085 [Listonella phage phiHSIC] ref|YP_468629.1| hypothetical protein 33.23 641 391 9 37125 35314 RHE_CH01094 [Rhizobium etli CFN 42] ref|YP_002280249.1| hypothetical protein 31.65 654 397 6 37125 35314 Rleg2_0727 [Rhizobium leguminosarum bv. trifolii ref|YP_769515.1| hypothetical protein 31.65 654 393 11 37050 35251 RL3937 [Rhizobium leguminosarum bv. viciae 3841] ref|ZP_06361168.1| conserved hypothetical 40.16 371 221 4 28854 27745 protein [Rhodopseudomonas palustris DX-1] ref|ZP_06361168.1| conserved hypothetical 44.32 176 93 3 29652 29140 protein [Rhodopseudomonas palustris DX-1] ref|ZP_02961020.1| hypothetical protein 37.97 403 244 7 12315 13505 PROSTU_03006 [Providencia stuartii ATCC 25827] ref|ZP_02961020.1| hypothetical protein 43.52 108 61 1 11993 12316 PROSTU_03006 [Providencia stuartii ATCC 25827] ref|ZP_01234562.1| putative ATP- 36.39 404 250 7 12315 13505 dependent helicase [Vibrio angustum S14] ref|ZP_01234562.1| putative ATP- 41.82 110 64 1 11996 12325 dependent helicase [Vibrio angustum S14] ref|YP_002263457.1| putative helicase 38.17 393 237 7 12297 13457 (DEAD/DEAH box helicase) [Aliivibrio salmonicida ref|YP_002263457.1| putative helicase 44.44 108 60 1 11996 12319 (DEAD/DEAH box helicase) [Aliivibrio salmonicida ref|YP_002155626.1| DNA or RNA helicase 37.47 403 246 7 12315 13505 [Vibrio fischeri MJ11] ref|YP_002155626.1| DNA or RNA helicase 43.52 108 61 1 11996 12319 [Vibrio fischeri MJ11] ref|YP_204247.1| ATP-dependet helicase 37.47 403 246 7 12315 13505 [Vibrio fischeri ES114] ref|YP_204247.1| ATP-dependet helicase 43.52 108 61 1 11996 12319 [Vibrio fischeri ES114] ref|YP_003333937.1| type III restriction 38.71 403 241 7 12315 13505 protein res subunit [Dickeya dadantii Ech586] ref|YP_003333937.1| type III restriction 45.83 96 52 1 11996 12283 protein res subunit [Dickeya dadantii Ech586] ref|ZP_02195032.1| helicase-related 36.45 428 265 9 12315 13577 protein [Vibrio sp. AND4] ref|ZP_02195032.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio sp. AND4] ref|ZP_01160173.1| putative ATP- 35.64 404 253 7 12315 13505 dependent helicase [Photobacterium sp. SKA34] ref|ZP_01160173.1| putative ATP- 41.82 110 64 1 11996 12325 dependent helicase [Photobacterium sp. SKA34] ref|ZP_06125419.1| putative helicase, 35.80 405 254 7 12309 13505 ATP-dependent [Providencia rettgeri DSM 1131] ref|ZP_06125419.1| putative helicase, 44.44 108 60 1 11993 12316 ATP-dependent [Providencia rettgeri DSM 1131] ref|ZP_03345188.1| putative helicase 37.22 403 247 7 12315 13505 [Salmonella enterica subsp. enterica serovar Typhi ref|ZP_03345188.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Typhi ref|ZP_02667261.1| putative helicase 37.98 387 234 6 12315 13457 [Salmonella enterica subsp. enterica serovar ref|ZP_02667261.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar ref|YP_149939.1| putative helicase 37.98 387 234 6 12315 13457 [Salmonella enterica subsp. enterica serovar ref|YP_149939.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar ref|ZP_06155453.1| putative ATP- 36.34 388 240 6 12315 13457 dependent helicase [Photobacterium damselae subsp. ref|ZP_06155453.1| putative ATP- 40.91 110 65 1 11996 12325 dependent helicase [Photobacterium damselae subsp. ref|ZP_03220222.1| putative helicase 37.98 387 234 6 12315 13457 [Salmonella enterica subsp. enterica serovar Javiana ref|ZP_03220222.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Javiana ref|YP_001587034.1| hypothetical protein 37.73 387 235 6 12315 13457 SPAB_00777 [Salmonella enterica subsp. enterica ref|YP_001587034.1| hypothetical protein 42.73 110 63 1 11996 12325 SPAB_00777 [Salmonella enterica subsp. enterica ref|YP_002244308.1| putative helicase 37.73 387 235 6 12315 13457 [Salmonella enterica subsp. enterica serovar ref|YP_002244308.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar ref|YP_002227157.1| putative helicase 37.73 387 235 6 12315 13457 [Salmonella enterica subsp. enterica serovar ref|YP_002227157.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar ref|ZP_03213834.1| putative helicase 37.73 387 235 6 12315 13457 [Salmonella enterica subsp. enterica serovar Virchow ref|ZP_03213834.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Virchow ref|NP_456781.1| putative helicase 37.73 387 235 6 12315 13457 [Salmonella enterica subsp. enterica serovar Typhi ref|NP_456781.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Typhi ref|YP_002147196.1| putative helicase 37.73 387 235 6 12315 13457 [Salmonella enterica subsp. enterica serovar Agona ref|YP_002147196.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Agona ref|ZP_02654653.1| putative helicase 37.73 387 235 6 12315 13457 [Salmonella enterica subsp. enterica serovar Kentucky ref|ZP_02654653.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Kentucky ref|ZP_06639525.1| conserved hypothetical 37.87 404 245 7 12312 13505 protein [Serratia odorifera DSM 4582] ref|ZP_06639525.1| conserved hypothetical 41.12 107 63 1 11996 12316 protein [Serratia odorifera DSM 4582] ref|YP_003211214.1| Uncharacterized 37.97 403 244 7 12315 13505 protein yejH [Cronobacter turicensis z3032] ref|YP_003211214.1| Uncharacterized 42.59 108 62 1 11996 12319 protein yejH [Cronobacter turicensis z3032] ref|ZP_05877188.1| helicase-related 35.28 428 270 9 12315 13577 protein [Vibrio furnissii CIP 102972] ref|ZP_05877188.1| helicase-related 41.82 110 64 1 11996 12325 protein [Vibrio furnissii CIP 102972] ref|ZP_02683731.1| putative helicase 37.47 387 236 6 12315 13457 [Salmonella enterica subsp. enterica serovar Hadar ref|ZP_02683731.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Hadar ref|YP_129752.1| putative ATP- 35.31 405 255 7 12312 13505 dependent helicase [Photobacterium profundum SS9] ref|YP_129752.1| putative ATP- 41.12 107 63 1 11996 12316 dependent helicase [Photobacterium profundum SS9] ref|YP_003365861.1| putative helicase 37.47 403 246 7 12315 13505 [Citrobacter rodentium ICC168] ref|YP_003365861.1| putative helicase 43.52 108 61 1 11996 12319 [Citrobacter rodentium ICC168] ref|YP_217227.1| putative ATP- 37.47 387 236 6 12315 13457 dependent helicase [Salmonella enterica subsp. enterica ref|YP_217227.1| putative ATP- 42.73 110 63 1 11996 12325 dependent helicase [Salmonella enterica subsp. enterica ref|YP_001401684.1| putative helicase 37.87 404 245 7 12312 13505 [Yersinia pseudotuberculosis IP 31758] ref|YP_001401684.1| putative helicase 40.19 107 64 1 11996 12316 [Yersinia pseudotuberculosis IP 31758] ref|NP_670218.1| ATP-dependent 37.87 404 245 7 12312 13505 helicase [Yersinia pestis KIM 10] ref|NP_670218.1| ATP-dependent 40.19 107 64 1 11996 12316 helicase [Yersinia pestis KIM 10] ref|YP_001445844.1| hypothetical protein 35.75 428 268 9 12315 13577 VIBHAR_02656 [Vibrio harveyi ATCC BAA-1116] ref|YP_001445844.1| hypothetical protein 41.82 110 64 1 11996 12325 VIBHAR_02656 [Vibrio harveyi ATCC BAA-1116] ref|NP_934217.1| DNA or RNA helicase 36.60 388 239 7 12315 13457 [Vibrio vulnificus YJ016] ref|NP_934217.1| DNA or RNA helicase 41.82 110 64 1 11996 12325 [Vibrio vulnificus YJ016] ref|ZP_01218531.1| putative ATP- 35.31 405 255 7 12312 13505 dependent helicase [Photobacterium profundum 3TCK] ref|ZP_01218531.1| putative ATP- 41.12 107 63 1 11996 12316 dependent helicase [Photobacterium profundum 3TCK] ref|YP_069832.1| putative DEAD box 37.87 404 245 7 12312 13505 helicase family protein [Yersinia pseudotuberculosis ref|YP_069832.1| putative DEAD box 40.19 107 64 1 11996 12316 helicase family protein [Yersinia pseudotuberculosis ref|ZP_04619081.1| hypothetical protein 37.87 404 245 7 12312 13505 yaldo0001_20880 [Yersinia aldovae ATCC 35236] ref|ZP_04619081.1| hypothetical protein 40.19 107 64 1 11996 12316 yaldo0001_20880 [Yersinia aldovae ATCC 35236] ref|ZP_04633499.1| hypothetical protein 38.37 404 243 7 12312 13505 yfred0001_40330 [Yersinia frederiksenii ATCC ref|ZP_04633499.1| hypothetical protein 40.19 107 64 1 11996 12316 yfred0001_40330 [Yersinia frederiksenii ATCC ref|ZP_04616780.1| hypothetical protein 38.12 404 244 7 12312 13505 yruck0001_10270 [Yersinia ruckeri ATCC 29473] ref|ZP_04616780.1| hypothetical protein 42.06 107 62 1 11996 12316 yruck0001_10270 [Yersinia ruckeri ATCC 29473] ref|ZP_06053624.1| putative ATP- 36.97 403 248 7 12315 13505 dependent helicase [Grimontia hollisae CIP 101886] ref|ZP_06053624.1| putative ATP- 39.81 108 65 1 11996 12319 dependent helicase [Grimontia hollisae CIP 101886] ref|ZP_02661469.1| putative helicase 37.47 387 236 6 12315 13457 [Salmonella enterica subsp. enterica serovar ref|ZP_02661469.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar ref|ZP_06048813.1| helicase-related 34.58 454 290 10 12315 13655 protein [Vibrio cholerae CT 5369-93] ref|ZP_06048813.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio cholerae CT 5369-93] ref|ZP_05926045.1| helicase-related 34.80 454 289 10 12315 13655 protein [Vibrio sp. RC341] ref|ZP_05926045.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio sp. RC341] ref|ZP_04562718.1| conserved hypothetical 36.36 407 253 7 12315 13517 protein [Citrobacter sp. 30_2] ref|ZP_04562718.1| conserved hypothetical 42.59 108 62 1 11996 12319 protein [Citrobacter sp. 30_2] ref|YP_003017214.1| type III restriction 36.97 403 248 7 12315 13505 protein res subunit [Pectobacterium carotovorum ref|YP_003017214.1| type III restriction 41.12 107 63 1 11996 12316 protein res subunit [Pectobacterium carotovorum ref|ZP_06080609.1| helicase-related 34.80 454 289 10 12315 13655 protein [Vibrio sp. RC586] ref|ZP_06080609.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio sp. RC586] ref|ZP_05968474.1| putative helicase, 37.47 403 246 7 12315 13505 ATP-dependent [Enterobacter cancerogenus ATCC 35316] ref|ZP_05968474.1| putative helicase, 40.91 110 65 1 11996 12325 ATP-dependent [Enterobacter cancerogenus ATCC 35316] ref|ZP_03049176.1| putative helicase 37.47 387 236 6 12315 13457 [Escherichia coli E110019] ref|ZP_03049176.1| putative helicase 43.52 108 61 1 11996 12319 [Escherichia coli E110019] ref|ZP_06191030.1| type III restriction 37.62 404 246 7 12312 13505 protein res subunit [Serratia odorifera 4Rx13] ref|ZP_06191030.1| type III restriction 41.12 107 63 1 11996 12316 protein res subunit [Serratia odorifera 4Rx13] ref|NP_797593.1| helicase-related 35.98 428 267 9 12315 13577 protein [Vibrio parahaemolyticus RIMD 2210633] ref|NP_797593.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio parahaemolyticus RIMD 2210633] ref|ZP_06352119.2| putative helicase, 36.61 407 252 7 12315 13517 ATP-dependent [Citrobacter youngae ATCC 29220] ref|ZP_06352119.2| putative helicase, 42.59 108 62 1 11996 12319 ATP-dependent [Citrobacter youngae ATCC 29220] ref|ZP_04613347.1| hypothetical protein 38.12 404 244 7 12312 13505 yrohd0001_26030 [Yersinia rohdei ATCC 43380] ref|ZP_04613347.1| hypothetical protein 40.19 107 64 1 11996 12316 yrohd0001_26030 [Yersinia rohdei ATCC 43380] ref|ZP_05719867.1| helicase-related 37.11 388 237 7 12315 13457 protein [Vibrio mimicus VM603] ref|ZP_05719867.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio mimicus VM603] dbj|BAI55606.1| putative ATP- 37.73 387 235 6 12315 13457 dependent helicase [Escherichia coli SE15] dbj|BAI55606.1| putative ATP- 43.52 108 61 1 11996 12319 dependent helicase [Escherichia coli SE15] ref|YP_001569729.1| hypothetical protein 37.73 387 235 6 12315 13457 SARI_00664 [Salmonella enterica subsp. arizonae ref|YP_001569729.1| hypothetical protein 42.59 108 62 1 11996 12319 SARI_00664 [Salmonella enterica subsp. arizonae ref|YP_001452182.1| hypothetical protein 36.97 403 248 7 12315 13505 CKO_00592 [Citrobacter koseri ATCC BAA-895] ref|YP_001452182.1| hypothetical protein 43.52 108 61 1 11996 12319 CKO_00592 [Citrobacter koseri ATCC BAA-895] ref|YP_001479479.1| type III restriction 37.62 404 246 7 12312 13505 protein res subunit [Serratia proteamaculans 568] ref|YP_001479479.1| type III restriction 41.12 107 63 1 11996 12316 protein res subunit [Serratia proteamaculans 568] ref|ZP_01978844.1| DNA or RNA helicase 34.58 454 290 10 12315 13655 [Vibrio cholerae MZO-2] ref|ZP_01978844.1| DNA or RNA helicase 40.91 110 65 1 11996 12325 [Vibrio cholerae MZO-2] ref|ZP_06039032.1| helicase-related 37.11 388 237 7 12315 13457 protein [Vibrio mimicus MB-451] ref|ZP_06039032.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio mimicus MB-451] ref|YP_670125.1| hypothetical protein 37.73 387 235 6 12315 13457 ECP_2225 [Escherichia coli 536] ref|YP_670125.1| hypothetical protein 43.52 108 61 1 11996 12319 ECP_2225 [Escherichia coli 536] ref|YP_003286407.1| helicase-related 35.51 428 269 9 12315 13577 protein [Vibrio sp. Ex25] ref|YP_003286407.1| helicase-related 41.82 110 64 1 11996 12325 protein [Vibrio sp. Ex25] ref|ZP_04960385.1| ATP-dependent RNA 34.36 454 291 10 12315 13655 helicase, DEAD/DEAH box family [Vibrio cholerae ref|ZP_04960385.1| ATP-dependent RNA 40.91 110 65 1 11996 12325 helicase, DEAD/DEAH box family [Vibrio cholerae ref|YP_001005731.1| putative DEAD box 38.12 404 244 7 12312 13505 helicase family protein [Yersinia enterocolitica ref|YP_001005731.1| putative DEAD box 40.19 107 64 1 11996 12316 helicase family protein [Yersinia enterocolitica ref|ZP_04418721.1| helicase-related 34.36 454 291 10 12315 13655 protein [Vibrio cholerae 12129(1)] ref|ZP_04418721.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio cholerae 12129(1)] ref|ZP_04410188.1| helicase-related 34.36 454 291 10 12315 13655 protein [Vibrio cholerae TM 11079- 80] ref|ZP_04410188.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio cholerae TM 11079- 80] ref|ZP_01950681.1| ATP-dependent RNA 34.36 454 291 10 12315 13655 helicase, DEAD/DEAH box family [Vibrio cholerae 1587] ref|ZP_01950681.1| ATP-dependent RNA 40.91 110 65 1 11996 12325 helicase, DEAD/DEAH box family [Vibrio cholerae 1587] ref|YP_001463537.1| putative helicase 37.47 387 236 6 12315 13457 [Escherichia coli E24377A] ref|YP_001463537.1| putative helicase 43.52 108 61 1 11996 12319 [Escherichia coli E24377A] ref|YP_689683.1| putative ATP- 37.47 387 236 6 12315 13457 dependent helicase [Shigella flexneri 5 str. 8401] ref|YP_689683.1| putative ATP- 43.52 108 61 1 11996 12319 dependent helicase [Shigella flexneri 5 str. 8401] ref|NP_416689.1| predicted ATP- 37.47 387 236 6 12315 13457 dependent DNA or RNA helicase [Escherichia coli str. K-12 ref|NP_416689.1| predicted ATP- 43.52 108 61 1 11996 12319 dependent DNA or RNA helicase [Escherichia coli str. K-12 ref|YP_003468785.1| putative ATP- 36.22 392 244 6 12315 13472 dependent helicase with nucleoside triP hydrolase domain ref|YP_003468785.1| putative ATP- 41.12 107 63 1 11996 12316 dependent helicase with nucleoside triP hydrolase domain ref|ZP_04404492.1| helicase-related 34.36 454 291 10 12315 13655 protein [Vibrio cholerae TMA 21] ref|ZP_04404492.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio cholerae TMA 21] ref|ZP_04005046.1| ATP-dependent 37.73 387 235 6 12315 13457 helicase [Escherichia coli 83972] ref|ZP_04005046.1| ATP-dependent 42.59 108 62 1 11996 12319 helicase [Escherichia coli 83972] ref|ZP_01983341.1| putative DNA or RNA 34.36 454 291 10 12315 13655 helicase [Vibrio cholerae 623-39] ref|ZP_01983341.1| putative DNA or RNA 40.91 110 65 1 11996 12325 helicase [Vibrio cholerae 623-39] ref|ZP_06033549.1| helicase-related 37.11 388 237 7 12315 13457 protein [Vibrio mimicus VM223] ref|ZP_06033549.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio mimicus VM223] ref|NP_754607.1| hypothetical protein 37.73 387 235 6 12315 13457 c2721 [Escherichia coli CFT073] ref|NP_754607.1| hypothetical protein 42.59 108 62 1 11996 12319 c2721 [Escherichia coli CFT073] ref|YP_001437156.1| hypothetical protein 37.47 403 246 7 12315 13505 ESA_01052 [Cronobacter sakazakii ATCC BAA-894] ref|YP_001437156.1| hypothetical protein 42.59 108 62 1 11996 12319 ESA_01052 [Cronobacter sakazakii ATCC BAA-894] ref|YP_001458984.1| putative helicase 37.47 387 236 6 12315 13457 [Escherichia coli HS] ref|YP_001458984.1| putative helicase 43.52 108 61 1 11996 12319 [Escherichia coli HS] ref|ZP_06654124.1| helicase [Escherichia 37.47 387 236 6 12315 13457 coli B354] ref|ZP_06654124.1| helicase [Escherichia 43.52 108 61 1 11996 12319 coli B354] ref|ZP_06658113.1| helicase [Escherichia 37.47 387 236 6 12315 13457 coli B185] ref|ZP_06658113.1| helicase [Escherichia 43.52 108 61 1 11996 12319 coli B185] ref|YP_002408285.1| putative nucleic acid 37.47 387 236 6 12315 13457 ATP-dependent helicase [Escherichia coli IAI39] ref|YP_002408285.1| putative nucleic acid 43.52 108 61 1 11996 12319 ATP-dependent helicase [Escherichia coli IAI39] ref|NP_288767.1| putative ATP- 37.47 387 236 6 12315 13457 dependent helicase [Escherichia coli O157:H7 EDL933] ref|NP_288767.1| putative ATP- 43.52 108 61 1 11996 12319 dependent helicase [Escherichia coli O157:H7 EDL933] ref|ZP_05945679.1| helicase-related 34.62 439 280 9 12315 13610 protein [Vibrio orientalis CIP 102891] ref|ZP_05945679.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio orientalis CIP 102891] ref|ZP_05435996.1| predicted ATP- 37.47 387 236 6 12315 13457 dependet helicase [Escherichia sp. 4_1_40B] ref|ZP_05435996.1| predicted ATP- 43.52 108 61 1 11996 12319 dependet helicase [Escherichia sp. 4_1_40B] ref|YP_002398545.1| putative nucleic acid 37.47 387 236 6 12315 13457 ATP-dependent helicase [Escherichia coli ED1a] ref|YP_002398545.1| putative nucleic acid 43.52 108 61 1 11996 12319 ATP-dependent helicase [Escherichia coli ED1a] ref|YP_002329837.1| predicted ATP- 37.47 387 236 6 12315 13457 dependet helicase [Escherichia coli O127:H6 str. ref|YP_002329837.1| predicted ATP- 43.52 108 61 1 11996 12319 dependet helicase [Escherichia coli O127:H6 str. emb|CBG35250.1| putative helicase 37.47 387 236 6 12315 13457 [Escherichia coli 042] emb|CBG35250.1| putative helicase 43.52 108 61 1 11996 12319 [Escherichia coli 042] ref|YP_311124.1| putative ATP- 37.21 387 237 6 12315 13457 dependent helicase [Shigella sonnei Ss046] ref|YP_311124.1| putative ATP- 44.44 108 60 1 11996 12319 dependent helicase [Shigella sonnei Ss046] ref|ZP_06182173.1| helicase-related 35.05 428 271 9 12315 13577 protein [Vibrio alginolyticus 40B] ref|ZP_06182173.1| helicase-related 41.82 110 64 1 11996 12325 protein [Vibrio alginolyticus 40B] ref|YP_002383391.1| putative nucleic acid 37.47 387 236 6 12315 13457 ATP-dependent helicase [Escherichia fergusonii ref|YP_002383391.1| putative nucleic acid 43.52 108 61 1 11996 12319 ATP-dependent helicase [Escherichia fergusonii ref|ZP_01956145.1| DNA or RNA helicase 36.86 388 238 7 12315 13457 [Vibrio cholerae MZO-3] ref|ZP_01956145.1| DNA or RNA helicase 40.91 110 65 1 11996 12325 [Vibrio cholerae MZO-3] ref|ZP_04413136.1| helicase-related 34.36 454 291 10 12315 13655 protein [Vibrio cholerae bv. albensis VL426] ref|ZP_04413136.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio cholerae bv. albensis VL426] ref|YP_003259295.1| type III restriction 36.72 403 249 7 12315 13505 protein res subunit [Pectobacterium wasabiae ref|YP_003259295.1| type III restriction 40.19 107 64 1 11996 12316 protein res subunit [Pectobacterium wasabiae emb|CBK87212.1| DNA or RNA 36.63 404 250 7 12312 13505 helicases of superfamily II [Enterobacter cloacae NCTC 9394] emb|CBK87212.1| DNA or RNA 40.91 110 65 1 11996 12325 helicases of superfamily II [Enterobacter cloacae NCTC 9394] ref|YP_402562.1| putative ATP- 37.47 387 236 6 12315 13457 dependent helicase [Shigella dysenteriae Sd197] ref|YP_402562.1| putative ATP- 42.59 108 62 1 11996 12319 dependent helicase [Shigella dysenteriae Sd197] gb|ACI81269.1| putative ATP- 37.21 387 237 6 12315 13457 dependent helicase [Escherichia coli] gb|ACI81269.1| putative ATP- 43.52 108 61 1 11996 12319 dependent helicase [Escherichia coli] ref|YP_960220.1| type III restriction 36.76 408 247 10 12315 13505 enzyme, res subunit [Marinobacter aquaeolei VT8] ref|YP_960220.1| type III restriction 37.96 108 67 1 11996 12319 enzyme, res subunit [Marinobacter aquaeolei VT8] ref|ZP_01681930.1| ATP-dependent RNA 34.14 454 292 10 12315 13655 helicase, DEAD/DEAH box family [Vibrio cholerae V52] ref|ZP_01681930.1| ATP-dependent RNA 40.91 110 65 1 11996 12325 helicase, DEAD/DEAH box family [Vibrio cholerae V52] ref|NP_231273.1| helicase-related 34.14 454 292 10 12315 13655 protein [Vibrio cholerae O1 biovar El Tor str. N16961] ref|NP_231273.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio cholerae O1 biovar El Tor str. N16961] ref|ZP_04397756.1| helicase-related 34.14 454 292 10 12315 13655 protein [Vibrio cholerae BX 330286] ref|ZP_04397756.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio cholerae BX 330286] ref|ZP_03066501.1| putative helicase 37.21 387 237 6 12315 13457 [Shigella dysenteriae 1012] ref|ZP_03066501.1| putative helicase 43.52 108 61 1 11996 12319 [Shigella dysenteriae 1012] ref|YP_001744380.1| putative helicase 37.47 387 236 6 12315 13457 [Escherichia coli SMS- 3-5] ref|YP_001744380.1| putative helicase 43.52 108 61 1 11996 12319 [Escherichia coli SMS- 3-5] ref|NP_708083.1| putative ATP- 37.21 387 237 6 12315 13457 dependent helicase [Shigella flexneri 2a str. 301] ref|NP_708083.1| putative ATP- 43.52 108 61 1 11996 12319 dependent helicase [Shigella flexneri 2a str. 301] ref|ZP_03842064.1| helicase [Proteus 36.99 392 241 6 12315 13472 mirabilis ATCC 29906] ref|ZP_03842064.1| helicase [Proteus 42.59 108 62 1 11996 12319 mirabilis ATCC 29906] ref|YP_002150583.1| helicase [Proteus 36.99 392 241 6 12315 13472 mirabilis HI4320] ref|YP_002150583.1| helicase [Proteus 42.59 108 62 1 11996 12319 mirabilis HI4320] ref|YP_003296361.1| DNA or RNA 38.24 387 233 6 12315 13457 helicases of superfamily II [Edwardsiella tarda EIB202] ref|YP_003296361.1| DNA or RNA 42.06 107 62 1 11996 12316 helicases of superfamily II [Edwardsiella tarda EIB202] ref|ZP_02827406.1| putative helicase 37.47 387 236 6 12315 13457 [Escherichia coli O157:H7 str. EC508] ref|ZP_02827406.1| putative helicase 43.52 108 61 1 11996 12319 [Escherichia coli O157:H7 str. EC508] ref|ZP_04637851.1| hypothetical protein 38.12 404 244 7 12312 13505 yinte0001_11550 [Yersinia intermedia ATCC 29909] ref|ZP_04637851.1| hypothetical protein 40.19 107 64 1 11996 12316 yinte0001_11550 [Yersinia intermedia ATCC 29909] ref|ZP_01078151.1| putative helicase 33.55 453 295 8 12315 13655 [Marinomonas sp. MED121] ref|ZP_01078151.1| putative helicase 41.28 109 64 1 11993 12319 [Marinomonas sp. MED121] ref|YP_001177496.1| type III restriction 36.63 404 250 7 12312 13505 enzyme, res subunit [Enterobacter sp. 638] ref|YP_001177496.1| type III restriction 40.91 110 65 1 11996 12325 enzyme, res subunit [Enterobacter sp. 638] ref|ZP_03027279.1| putative helicase 37.21 387 237 6 12315 13457 [Escherichia coli B7A] ref|ZP_03027279.1| putative helicase 43.52 108 61 1 11996 12319 [Escherichia coli B7A] ref|ZP_04622971.1| hypothetical protein 37.62 404 246 7 12312 13505 ykris0001_4070 [Yersinia kristensenii ATCC 33638] ref|ZP_04622971.1| hypothetical protein 40.19 107 64 1 11996 12316 ykris0001_4070 [Yersinia kristensenii ATCC 33638] ref|YP_003531677.1| Uncharacterized 36.86 407 251 8 12315 13517 protein yejH [Erwinia amylovora CFBP1430] ref|YP_003531677.1| Uncharacterized 44.86 107 59 1 11996 12316 protein yejH [Erwinia amylovora CFBP1430] ref|YP_050835.1| putative helicase 36.99 392 241 6 12315 13472 [Pectobacterium atrosepticum SCRI1043] ref|YP_050835.1| putative helicase 41.12 107 63 1 11996 12316 [Pectobacterium atrosepticum SCRI1043] ref|ZP_06715404.1| putative helicase, 36.72 403 249 7 12315 13505 ATP-dependent [Edwardsiella tarda ATCC 23685] ref|ZP_06715404.1| putative helicase, 42.99 107 61 1 11996 12316 ATP-dependent [Edwardsiella tarda ATCC 23685] ref|ZP_01066377.1| helicase-related 34.35 428 274 9 12315 13577 protein [Vibrio sp. MED222] ref|ZP_01066377.1| helicase-related 40.00 110 66 1 11996 12325 protein [Vibrio sp. MED222] ref|ZP_05887740.1| helicase-related 34.50 429 274 9 12315 13580 protein [Vibrio coralliilyticus ATCC BAA-450] ref|ZP_05887740.1| helicase-related 41.82 110 64 1 11996 12325 protein [Vibrio coralliilyticus ATCC BAA-450] ref|ZP_01991276.1| DNA or RNA helicase 37.40 385 234 7 12315 13448 [Vibrio parahaemolyticus AQ3810] ref|ZP_01991276.1| DNA or RNA helicase 40.91 110 65 1 11996 12325 [Vibrio parahaemolyticus AQ3810] ref|YP_003494744.1| type III restriction 37.08 391 230 12 12312 13436 protein res subunit [Thioalkalivibrio sp. K90mix] ref|YP_003494744.1| type III restriction 47.27 110 52 2 11999 12310 protein res subunit [Thioalkalivibrio sp. K90mix] ref|YP_003520872.1| YejH [Pantoea 34.98 466 288 12 12312 13664 ananatis LMG 20103] ref|YP_003520872.1| YejH [Pantoea 40.37 109 65 1 11996 12322 ananatis LMG 20103] ref|YP_408545.1| putative ATP- 37.21 387 237 6 12315 13457 dependent helicase [Shigella boydii Sb227] ref|YP_408545.1| putative ATP- 43.52 108 61 1 11996 12319 dependent helicase [Shigella boydii Sb227] emb|CBA72544.1| helicase 37.47 387 236 6 12315 13457 [Arsenophonus nasoniae] emb|CBA72544.1| helicase 41.12 107 63 1 11996 12316 [Arsenophonus nasoniae] gb|ADF63037.1| putative helicase 36.88 404 249 7 12312 13505 [Enterobacter cloacae subsp. cloacae ATCC 13047] gb|ADF63037.1| putative helicase 40.91 110 65 1 11996 12325 [Enterobacter cloacae subsp. cloacae ATCC 13047] ref|YP_001336265.1| putative ATP- 37.72 403 245 7 12315 13505 dependent helicase [Klebsiella pneumoniae subsp. ref|YP_001336265.1| putative ATP- 40.91 110 65 1 11996 12325 dependent helicase [Klebsiella pneumoniae subsp. ref|YP_002648342.1| Putative ATP- 36.12 407 254 8 12315 13517 dependent helicase [Erwinia pyrifoliae Ep1/96] ref|YP_002648342.1| Putative ATP- 45.79 107 58 1 11996 12316 dependent helicase [Erwinia pyrifoliae Ep1/96] ref|YP_002237396.1| putative helicase 37.72 403 245 7 12315 13505 [Klebsiella pneumoniae 342] ref|YP_002237396.1| putative helicase 40.91 110 65 1 11996 12325 [Klebsiella pneumoniae 342] ref|ZP_01616973.1| putative ATP- 33.85 455 292 11 12315 13652 dependent helicase [marine gamma proteobacterium HTCC2143] ref|ZP_01616973.1| putative ATP- 42.06 107 62 1 11996 12316 dependent helicase [marine gamma proteobacterium HTCC2143] ref|ZP_01893164.1| putative ATP- 35.28 411 252 8 12315 13505 dependent helicase with nucleoside triP hydrolase domain ref|ZP_01893164.1| putative ATP- 38.89 108 66 1 11996 12319 dependent helicase with nucleoside triP hydrolase domain ref|ZP_03320542.1| hypothetical protein 34.83 422 269 8 12315 13562 PROVALCAL_03503 [Providencia alcalifaciens DSM ref|ZP_03320542.1| hypothetical protein 41.82 110 64 1 11996 12325 PROVALCAL_03503 [Providencia alcalifaciens DSM ref|ZP_03825744.1| putative helicase 36.72 403 249 7 12315 13505 [Pectobacterium carotovorum subsp. brasiliensis ref|ZP_03825744.1| putative helicase 40.19 107 64 1 11996 12316 [Pectobacterium carotovorum subsp. brasiliensis ref|ZP_01166590.1| putative ATP- 35.41 401 251 8 12294 13472 dependent helicase [Oceanospirillum sp. MED92] ref|ZP_01166590.1| putative ATP- 37.17 113 71 1 11978 12316 dependent helicase [Oceanospirillum sp. MED92] ref|ZP_06547896.1| DNA or RNA helicase, 37.72 403 245 7 12315 13505 superfamily II [Klebsiella sp. 1_1_55] ref|ZP_06547896.1| DNA or RNA helicase, 40.91 110 65 1 11996 12325 superfamily II [Klebsiella sp. 1_1_55] ref|YP_003040502.1| hypothetical protein 35.06 405 255 7 12315 13505 PAU_01666 [Photorhabdus asymbiotica] ref|YP_003040502.1| hypothetical protein 40.91 110 65 1 11996 12325 PAU_01666 [Photorhabdus asymbiotica] ref|ZP_04628275.1| hypothetical protein 37.87 404 245 7 12312 13505 yberc0001_27060 [Yersinia bercovieri ATCC 43970] ref|ZP_04628275.1| hypothetical protein 39.25 107 65 1 11996 12316 yberc0001_27060 [Yersinia bercovieri ATCC 43970] ref|YP_002311188.1| Helicase: Type III 36.12 407 254 7 12315 13517 restriction enzyme, res subunit: DEAD/DEAH box ref|YP_002311188.1| Helicase: Type III 42.86 105 60 2 11996 12310 restriction enzyme, res subunit: DEAD/DEAH box ref|ZP_00992578.1| helicase-related 34.11 428 275 9 12315 13577 protein [Vibrio splendidus 12B01] ref|ZP_00992578.1| helicase-related 40.00 110 66 1 11996 12325 protein [Vibrio splendidus 12B01] ref|YP_002417462.1| helicase-like protein 33.64 428 277 9 12315 13577 [Vibrio splendidus LGP32] ref|YP_002417462.1| helicase-like protein 40.00 110 66 1 11996 12325 [Vibrio splendidus LGP32] ref|ZP_04640356.1| hypothetical protein 37.62 404 246 7 12312 13505 ymoll0001_26590 [Yersinia mollaretii ATCC 43969] ref|ZP_04640356.1| hypothetical protein 39.25 107 65 1 11996 12316 ymoll0001_26590 [Yersinia mollaretii ATCC 43969] ref|NP_930102.1| hypothetical protein 35.24 403 255 7 12315 13505 plu2868 [Photorhabdus luminescens subsp. laumondii ref|NP_930102.1| hypothetical protein 40.00 110 66 1 11996 12325 plu2868 [Photorhabdus luminescens subsp. laumondii ref|YP_001473601.1| type III restriction 36.12 407 254 7 12315 13517 enzyme, res subunit [Shewanella sediminis HAW-EB3] ref|YP_001473601.1| type III restriction 39.45 109 66 2 11996 12322 enzyme, res subunit [Shewanella sediminis HAW-EB3] ref|YP_750157.1| type III restriction 35.33 484 297 16 12315 13718 enzyme, res subunit [Shewanella frigidimarina ref|YP_750157.1| type III restriction 36.70 109 69 2 11996 12322 enzyme, res subunit [Shewanella frigidimarina ref|YP_001502414.1| type III restriction 33.68 484 303 12 12315 13712 protein res subunit [Shewanella pealeana ATCC ref|YP_001502414.1| type III restriction 40.95 105 62 2 11996 12310 protein res subunit [Shewanella pealeana ATCC ref|ZP_01738006.1| putative ATP- 34.55 411 255 8 12315 13505 dependent helicase with nucleoside triP hydrolase domain ref|ZP_01738006.1| putative ATP- 39.81 108 65 1 11996 12319 dependent helicase with nucleoside triP hydrolase domain ref|YP_572900.1| type III restriction 36.75 400 230 10 12327 13457 enzyme, res subunit [Chromohalobacter salexigens ref|YP_572900.1| type III restriction 41.67 108 63 1 11996 12319 enzyme, res subunit [Chromohalobacter salexigens ref|ZP_01217250.1| putative ATP- 34.11 428 276 8 12315 13580 dependent helicase [Psychromonas sp. CNPT3] ref|ZP_01217250.1| putative ATP- 40.91 110 65 1 11996 12325 dependent helicase [Psychromonas sp. CNPT3] ref|ZP_01614134.1| putative ATP- 36.62 385 238 6 12321 13457 dependent helicase with nucleoside triP hydrolase domain ref|ZP_01614134.1| putative ATP- 42.31 104 60 1 11996 12307 dependent helicase with nucleoside triP hydrolase domain ref|ZP_01815643.1| DNA or RNA helicase 33.88 428 276 9 12315 13577 [Vibrionales bacterium SWAT-3] ref|ZP_01815643.1| DNA or RNA helicase 40.00 110 66 1 11996 12325 [Vibrionales bacterium SWAT-3] ref|ZP_05119245.1| ATP-dependent rna 35.31 388 244 7 12315 13457 helicase, dead/deah box family [Vibrio ref|ZP_05119245.1| ATP-dependent rna 41.82 110 64 1 11996 12325 helicase, dead/deah box family [Vibrio ref|NP_718328.1| helicase [Shewanella 34.38 413 262 8 12315 13526 oneidensis MR-1] ref|NP_718328.1| helicase [Shewanella 46.07 89 48 1 11993 12259 oneidensis MR-1] ref|ZP_03806120.1| hypothetical protein 36.22 392 244 6 12315 13472 PROPEN_04520 [Proteus penneri ATCC 35198] ref|ZP_03806120.1| hypothetical protein 40.19 107 64 1 11996 12316 PROPEN_04520 [Proteus penneri ATCC 35198] ref|ZP_02158478.1| helicase [Shewanella 35.63 407 256 7 12315 13517 benthica KT99] ref|ZP_02158478.1| helicase [Shewanella 37.61 109 68 2 11996 12322 benthica KT99] ref|YP_003556546.1| helicase [Shewanella 35.14 407 258 7 12315 13517 violacea DSS12] ref|YP_003556546.1| helicase [Shewanella 38.53 109 67 2 11996 12322 violacea DSS12] ref|ZP_05730923.1| type III restriction 36.63 404 249 9 12315 13505 protein res subunit [Pantoea sp. At-9b] ref|ZP_05730923.1| type III restriction 42.99 107 61 1 11996 12316 protein res subunit [Pantoea sp. At-9b] ref|YP_870159.1| type III restriction 34.87 413 260 8 12315 13526 enzyme, res subunit [Shewanella sp. ANA- 3] ref|YP_870159.1| type III restriction 46.59 88 47 1 11996 12259 enzyme, res subunit [Shewanella sp. ANA- 3] ref|YP_734491.1| type III restriction 34.62 413 261 8 12315 13526 enzyme, res subunit [Shewanella sp. MR-4] ref|YP_734491.1| type III restriction 46.59 88 47 1 11996 12259 enzyme, res subunit [Shewanella sp. MR-4] ref|YP_002987959.1| type III restriction 37.50 392 239 6 12315 13472 protein res subunit [Dickeya dadantii Ech703] ref|YP_002987959.1| type III restriction 40.19 107 64 1 11996 12316 protein res subunit [Dickeya dadantii Ech703] ref|YP_738477.1| type III restriction 34.38 413 262 8 12315 13526 enzyme, res subunit [Shewanella sp. MR-7] ref|YP_738477.1| type III restriction 46.59 88 47 1 11996 12259 enzyme, res subunit [Shewanella sp. MR-7] ref|YP_001907200.1| Putative ATP- 35.63 407 256 8 12315 13517 dependent helicase [Erwinia tasmaniensis Et1/99] ref|YP_001907200.1| Putative ATP- 42.06 107 62 1 11996 12316 dependent helicase [Erwinia tasmaniensis Et1/99] ref|ZP_04919702.1| IS4 ORF [Vibrio 34.36 454 291 10 12315 13655 cholerae V51] ref|ZP_04919702.1| IS4 ORF [Vibrio 37.25 102 64 1 12020 12325 cholerae V51] ref|YP_001673921.1| type III restriction 35.63 407 256 7 12315 13517 protein res subunit [Shewanella halifaxensis ref|YP_001673921.1| type III restriction 43.18 88 50 1 11996 12259 protein res subunit [Shewanella halifaxensis ref|YP_942721.1| type III restriction 34.24 403 259 7 12315 13505 enzyme, res subunit [Psychromonas ingrahamii 37] ref|YP_942721.1| type III restriction 41.28 109 64 1 11996 12322 enzyme, res subunit [Psychromonas ingrahamii 37] ref|YP_857132.1| putative helicase, 35.22 389 244 7 12315 13457 ATP-dependent [Aeromonas hydrophila subsp. ref|YP_857132.1| putative helicase, 44.44 108 60 1 11993 12316 ATP-dependent [Aeromonas hydrophila subsp. ref|ZP_02901914.1| putative helicase 37.47 387 236 6 12315 13457 [Escherichia albertii TW07627] ref|ZP_02901914.1| putative helicase 38.00 100 62 1 12020 12319 [Escherichia albertii TW07627] ref|YP_001554221.1| type III restriction 35.35 413 258 8 12315 13526 protein res subunit [Shewanella baltica OS195] ref|YP_001554221.1| type III restriction 38.53 109 67 1 11996 12322 protein res subunit [Shewanella baltica OS195] ref|YP_963049.1| type III restriction 34.87 413 260 8 12315 13526 enzyme, res subunit [Shewanella sp. W3- 18-1] ref|YP_963049.1| type III restriction 42.55 94 54 1 11978 12259 enzyme, res subunit [Shewanella sp. W3- 18-1] ref|YP_002358450.1| type III restriction 35.11 413 259 8 12315 13526 protein res subunit [Shewanella baltica OS223] ref|YP_002358450.1| type III restriction 43.01 93 53 1 11996 12274 protein res subunit [Shewanella baltica OS223] ref|ZP_01707328.1| type III restriction 34.87 413 260 8 12315 13526 enzyme, res subunit [Shewanella putrefaciens 200] ref|ZP_01707328.1| type III restriction 42.55 94 54 1 11978 12259 enzyme, res subunit [Shewanella putrefaciens 200] ref|YP_001183870.1| type III restriction 34.87 413 260 8 12315 13526 enzyme, res subunit [Shewanella putrefaciens ref|YP_001183870.1| type III restriction 42.55 94 54 1 11978 12259 enzyme, res subunit [Shewanella putrefaciens ref|YP_001050129.1| type III restriction 35.11 413 259 8 12315 13526 protein res subunit [Shewanella baltica OS155] ref|YP_001050129.1| type III restriction 43.01 93 53 1 11996 12274 protein res subunit [Shewanella baltica OS155] ref|YP_001365953.1| type III restriction 35.35 413 258 8 12315 13526 protein res subunit [Shewanella baltica OS185] ref|YP_001365953.1| type III restriction 38.53 109 67 1 11996 12322 protein res subunit [Shewanella baltica OS185] ref|YP_001093658.1| type III restriction 36.12 407 254 8 12315 13517 enzyme, res subunit [Shewanella loihica PV-4] ref|YP_001093658.1| type III restriction 40.37 109 65 1 11996 12322 enzyme, res subunit [Shewanella loihica PV-4] ref|YP_563094.1| type III restriction 35.81 430 263 11 12315 13565 enzyme, res subunit [Shewanella denitrificans ref|YP_563094.1| type III restriction 38.53 109 67 2 11996 12322 enzyme, res subunit [Shewanella denitrificans ref|YP_001761097.1| type III restriction 34.40 407 261 8 12315 13517 protein res subunit [Shewanella woodyi ATCC 51908] ref|YP_001761097.1| type III restriction 41.51 106 62 2 11996 12313 protein res subunit [Shewanella woodyi ATCC 51908] ref|YP_001141517.1| ATP-dependent 35.22 389 244 6 12315 13457 helicase [Aeromonas salmonicida subsp. salmonicida A449] ref|YP_001141517.1| ATP-dependent 44.44 108 60 1 11993 12316 helicase [Aeromonas salmonicida subsp. salmonicida A449] ref|YP_340484.1| ATP-dependent 35.00 440 280 10 12321 13622 helicase [Pseudoalteromonas haloplanktis TAC125] ref|YP_340484.1| ATP-dependent 43.21 81 46 1 12065 12307 helicase [Pseudoalteromonas haloplanktis TAC125] ref|YP_002934010.1| hypothetical protein 37.57 362 220 6 12315 13382 NT01EI_2606 [Edwardsiella ictaluri 93-146] ref|YP_002934010.1| hypothetical protein 42.06 107 62 1 11996 12316 NT01EI_2606 [Edwardsiella ictaluri 93-146] ref|YP_001341391.1| type III restriction 34.19 389 248 7 12315 13457 protein res subunit [Marinomonas sp. MWYL1] ref|YP_001341391.1| type III restriction 36.70 109 69 1 11996 12322 protein res subunit [Marinomonas sp. MWYL1] ref|YP_663012.1| type III restriction 32.92 407 254 8 12294 13457 enzyme, res subunit [Pseudoalteromonas atlantica ref|YP_663012.1| type III restriction 38.89 108 66 1 11993 12316 enzyme, res subunit [Pseudoalteromonas atlantica ref|ZP_02335655.1| putative helicase 37.87 404 245 7 12312 13505 [Yersinia pestis FV-1] ref|ZP_02335655.1| putative helicase 34.72 72 47 1 12101 12316 [Yersinia pestis FV-1] ref|YP_003547295.1| type III restriction 33.41 431 277 12 12315 13577 protein res subunit [Coraliomargarita akajimensis ref|YP_003547295.1| type III restriction 45.83 96 52 2 11996 12283 protein res subunit [Coraliomargarita akajimensis ref|YP_927955.1| helicase [Shewanella 35.19 395 250 9 12315 13481 amazonensis SB2B] ref|YP_927955.1| helicase [Shewanella 36.70 109 69 1 11996 12322 amazonensis SB2B] ref|NP_970398.1| putative ATP- 34.53 391 246 10 12315 13457 dependent helicase [Bdellovibrio bacteriovorus HD100] ref|NP_970398.1| putative ATP- 45.83 96 52 1 11996 12283 dependent helicase [Bdellovibrio bacteriovorus HD100] ref|ZP_03829927.1| putative helicase 36.48 403 250 7 12315 13505 [Pectobacterium carotovorum subsp. carotovorum WPP14] ref|ZP_03829927.1| putative helicase 34.72 72 47 1 12101 12316 [Pectobacterium carotovorum subsp. carotovorum WPP14] gb|AAA16381.1| yejH [Escherichia coli] 38.51 296 176 4 12315 13184 gb|AAA16381.1| yejH [Escherichia coli] 43.52 108 61 1 11996 12319 ref|ZP_01899439.1| putative ATP- 36.81 383 236 8 12327 13457 dependent helicase with nucleoside triP hydrolasedomain ref|ZP_01899439.1| putative ATP- 30.99 71 49 1 12104 12316 dependent helicase with nucleoside triP hydrolasedomain ref|ZP_01132472.1| putative ATP- 36.72 384 236 7 12327 13457 dependent helicase with nucleoside triP hydrolase domain ref|ZP_01132472.1| putative ATP- 37.68 69 43 1 12101 12307 dependent helicase with nucleoside triP hydrolase domain ref|NP_102246.1| hypothetical protein 34.04 379 246 5 28866 27742 mll0452 [Mesorhizobium loti MAFF303099] ref|NP_102246.1| hypothetical protein 30.65 248 152 11 29661 28978 mll0452 [Mesorhizobium loti MAFF303099] ref|YP_003524538.1| phage uncharacterized 38.89 360 210 8 1474 425 protein [Sideroxydans lithotrophicus ES-1] ref|YP_003524538.1| phage uncharacterized 51.63 184 89 1 2893 2342 protein [Sideroxydans lithotrophicus ES-1] ref|YP_003004760.1| type III restriction 38.24 408 241 8 12315 13505 protein res subunit [Dickeya zeae Ech1591] ref|YP_003004760.1| type III restriction 33.73 166 103 3 11996 12472 protein res subunit [Dickeya zeae Ech1591] ref|YP_864936.1| hypothetical protein 33.41 416 256 8 36990 35806 Mmc1_1012 [Magnetococcus sp. MC-1] ref|YP_864936.1| hypothetical protein 29.07 172 102 7 35697 35242 Mmc1_1012 [Magnetococcus sp. MC-1] ref|ZP_05973724.1| putative helicase, 37.16 409 251 8 12297 13505 ATP-dependent [Providencia rustigianii DSM 4541] ref|ZP_05973724.1| putative helicase, 42.73 110 63 1 11996 12325 ATP-dependent [Providencia rustigianii DSM 4541] ref|ZP_05881861.1| helicase-related 36.36 407 252 8 12258 13457 protein [Vibrio metschnikovii CIP 69.14] ref|ZP_05881861.1| helicase-related 42.20 109 63 1 11996 12322 protein [Vibrio metschnikovii CIP 69.14] ref|ZP_05716951.1| helicase-related 37.31 394 240 8 12297 13457 protein [Vibrio mimicus VM573] ref|ZP_05716951.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio mimicus VM573] ref|ZP_05057345.1| Type III restriction 32.48 431 281 14 12315 13577 enzyme, res subunit family [Verrucomicrobiae ref|ZP_05057345.1| Type III restriction 41.67 96 56 1 11996 12283 enzyme, res subunit family [Verrucomicrobiae ref|ZP_01739797.1| putative ATP- 32.99 385 243 10 12327 13436 dependent helicase [Marinobacter sp. ELB17] ref|ZP_01739797.1| putative ATP- 38.05 113 64 1 11996 12316 dependent helicase [Marinobacter sp. ELB17] ref|ZP_05181869.1| hypothetical protein 36.28 328 207 6 28875 27898 Bru83_11056 [Brucella sp. 83/13] ref|ZP_05181869.1| hypothetical protein 33.94 165 108 4 29625 29134 Bru83_11056 [Brucella sp. 83/13] ref|ZP_06361166.1| conserved hypothetical 41.96 336 180 5 27272 26310 protein [Rhodopseudomonas palustris DX-1] ref|YP_003280885.1| pCQ3_36 29.10 725 448 21 2737 761 [Streptomyces sp. W9] ref|YP_769508.1| hypothetical protein 29.08 612 418 21 29631 27844 RL3930 [Rhizobium leguminosarum bv. viciae 3841] ref|ZP_02494554.1| ATPases with 25.60 828 539 19 37122 34870 chaperone activity, ATP-binding subunit [Burkholderia ref|YP_001063346.1| ATPases with 25.60 828 539 19 37122 34870 chaperone activity, ATP-binding subunit [Burkholderia ref|YP_002280258.1| hypothetical protein 28.13 647 442 22 29673 27802 Rleg2_0736 [Rhizobium leguminosarum bv. trifolii ref|ZP_06177758.1| helicase-related 36.03 408 258 8 12363 13577 protein [Vibrio harveyi 1DA3] ref|YP_001327489.1| hypothetical protein 33.42 377 250 5 28875 27748 Smed_1819 [Sinorhizobium medicae WSM419] ref|YP_001327489.1| hypothetical protein 27.54 167 121 4 29634 29134 Smed_1819 [Sinorhizobium medicae WSM419] ref|YP_769506.1| hypothetical protein 40.24 328 188 3 27275 26316 RL3928 [Rhizobium leguminosarum bv. viciae 3841] ref|YP_468637.1| hypothetical protein 40.56 323 185 3 27272 26325 RHE_CH01103 [Rhizobium etli CFN 42] ref|YP_672800.1| hypothetical protein 51.30 230 103 1 31062 30400 Meso_0231 [Mesorhizobium sp. BNC1] ref|YP_002826409.1| hypothetical protein 32.63 377 253 5 28875 27748 NGR_c18920 [Rhizobium sp. NGR234] ref|YP_002826409.1| hypothetical protein 31.45 159 109 3 29610 29134 NGR_c18920 [Rhizobium sp. NGR234] ref|ZP_03522929.1| hypothetical protein 39.14 327 192 3 27275 26316 RetlG_17541 [Rhizobium etli GR56] ref|ZP_05811994.1| protein of unknown 56.76 185 80 1 21202 20648 function DUF847 [Mesorhizobium opportunistum ref|YP_002280260.1| hypothetical protein 39.14 327 192 3 27275 26316 Rleg2_0738 [Rhizobium leguminosarum bv. trifolii ref|ZP_03383797.1| putative helicase 38.05 339 208 5 12447 13457 [Salmonella enterica subsp. enterica serovar Typhi ref|NP_102250.1| hypothetical protein 37.13 334 208 4 32487 31492 mll0457 [Mesorhizobium loti MAFF303099] ref|YP_917849.1| hypothetical protein 51.38 181 88 0 21202 20660 Pden_4087 [Paracoccus denitrificans PD1222] ref|ZP_03523887.1| hypothetical protein 29.60 500 332 18 29634 28195 RetlG_23247 [Rhizobium etli GR56] ref|YP_672802.1| hypothetical protein 41.03 234 137 2 30378 29680 Meso_0233 [Mesorhizobium sp. BNC1] ref|ZP_02494546.1| hypothetical protein 27.00 600 425 17 29601 27841 BpseN_34245 [Burkholderia pseudomallei NCTC 13177] ref|YP_001063338.1| hypothetical protein 27.00 600 425 17 29601 27841 BURPS668_A2344 [Burkholderia pseudomallei 668] ref|YP_672809.1| microcystin-dependent 40.51 274 157 8 22147 21344 protein-like [Mesorhizobium sp. BNC1] ref|YP_002601309.1| putative secretion 48.80 209 107 3 21202 20576 activating protein [Desulfobacterium autotrophicum ref|YP_002125131.1| phage uncharacterized 34.24 330 211 6 1375 404 protein [Alteromonas macleodii ‘Deep ecotype’] ref|YP_002125131.1| phage uncharacterized 30.84 107 74 0 2641 2321 protein [Alteromonas macleodii ‘Deep ecotype’] ref|YP_002497863.1| protein of unknown 48.97 194 98 2 21181 20603 function DUF847 [Methylobacterium nodulans ORS 2060] ref|YP_002500190.1| protein of unknown 54.07 172 79 2 21181 20666 function DUF847 [Methylobacterium nodulans ORS 2060] ref|YP_002500876.1| protein of unknown 52.27 176 84 2 21193 20666 function DUF847 [Methylobacterium nodulans ORS 2060] ref|YP_001353895.1| hypothetical protein 24.66 730 503 16 36900 34852 mma_2205 [Janthinobacterium sp. Marseille] ref|YP_002499091.1| protein of unknown 46.19 197 106 1 21193 20603 function DUF847 [Methylobacterium nodulans ORS 2060] ref|ZP_00209324.1| COG3926: Putative 46.49 185 99 1 21193 20639 secretion activating protein [Magnetospirillum ref|ZP_06361173.1| conserved hypothetical 37.12 326 203 4 32460 31489 protein [Rhodopseudomonas palustris DX-1] ref|YP_002495956.1| protein of unknown 52.33 172 82 2 21181 20666 function DUF847 [Methylobacterium nodulans ORS 2060] ref|YP_002499477.1| protein of unknown 50.29 175 87 1 21190 20666 function DUF847 [Methylobacterium nodulans ORS 2060] ref|YP_002497304.1| protein of unknown 51.74 172 83 1 21181 20666 function DUF847 [Methylobacterium nodulans ORS 2060] ref|ZP_06793097.1| hypothetical protein 45.81 203 110 1 21190 20582 BAZG_01351 [Brucella sp. NVSL 07-0026] ref|ZP_05168646.1| hypothetical protein 45.81 203 110 1 21190 20582 BpinM_07480 [Brucella pinnipedialis M163/99/10] ref|ZP_05163566.1| hypothetical protein 45.81 203 110 1 21190 20582 Bsuib55_12901 [Brucella suis bv. 5 str. 513] ref|YP_001592825.1| hypothetical protein 45.81 203 110 1 21190 20582 BCAN_A1001 [Brucella canis ATCC 23365] ref|YP_221702.1| secretion activator 45.81 203 110 1 21190 20582 protein [Brucella abortus bv. 1 str. 9- 941] ref|YP_002497710.1| protein of unknown 51.43 175 85 2 21190 20666 function DUF847 [Methylobacterium nodulans ORS 2060] ref|ZP_01870783.1| helicase-related 37.90 314 192 7 12648 13580 protein [Vibrio shilonii AK1] ref|YP_003366167.1| putative prophage 39.59 245 142 5 15941 16657 DNA methylase [Citrobacter rodentium ICC168] ref|ZP_05451234.1| hypothetical protein 45.32 203 111 1 21190 20582 Bneo5_12042 [Brucella neotomae 5K33] ref|YP_224274.1| putative helicase 47.01 251 130 5 8623 9366 subunit [Listonella phage phiHSIC] ref|YP_002732723.1| hypothetical protein 45.32 203 111 1 21190 20582 BMEA_A1023 [Brucella melitensis ATCC 23457] ref|ZP_01976451.1| DNA or RNA helicase 32.60 181 118 2 12315 12845 [Vibrio cholerae B33] ref|ZP_01976451.1| DNA or RNA helicase 40.91 110 65 1 11996 12325 [Vibrio cholerae B33] ref|ZP_05457454.1| hypothetical protein 45.32 203 111 1 21190 20582 BcetM4_12068 12068 [Brucella ceti M490/95/1] ref|ZP_03349713.1| putative helicase 40.59 271 159 4 12651 13457 [Salmonella enterica subsp. enterica serovar Typhi ref|NP_539912.1| secretion activator 44.55 202 112 1 21190 20585 protein [Brucella melitensis 16M] ref|ZP_05256839.1| gp10 [Bacteroides sp. 36.90 271 157 6 15896 16666 4_3_47FAA] ref|YP_100085.1| putative site-specific 36.90 271 157 6 15896 16666 DNA- methyltransferase [Bacteroides fragilis ref|YP_865634.1| hypothetical protein 34.10 346 224 9 28857 27832 Mmc1_1720 [Magnetococcus sp. MC-1] ref|ZP_04550445.1| gp10 [Bacteroides sp. 36.53 271 158 6 15896 16666 2_2_4] ref|ZP_05414506.1| DNA (cytosine-5-)- 38.02 263 152 6 15896 16651 methyltransferase [Bacteroides finegoldii DSM 17565] ref|NP_203459.1| virion structural 27.23 459 293 11 37041 35788 protein [Myxococcus phage Mx8] ref|ZP_03009853.1| hypothetical protein 37.64 263 153 7 15896 16651 BACCOP_017015 [Bacteroides coprocola DSM 17136] ref|ZP_03508429.1| hypothetical protein 38.61 259 155 2 27275 26511 RetlB5_25766 [Rhizobium etli Brasil 5] ref|NP_958114.1| gp10 [Burkholderia 38.06 247 145 5 15944 16660 phage Bcep43] ref|NP_705636.1| gp10 [Burkholderia 38.06 247 145 5 15944 16660 phage Bcep781] ref|YP_613683.1| hypothetical protein 46.12 219 106 4 10751 11371 TM1040_1688 [Ruegeria sp. TM1040] ref|YP_002501648.1| protein of unknown 46.89 177 93 2 21190 20663 function DUF847 [Methylobacterium nodulans ORS 2060] ref|ZP_03458262.1| hypothetical protein 36.88 263 155 7 15896 16651 BACEGG_01035 [Bacteroides eggerthii DSM 20697] ref|ZP_03208869.1| hypothetical protein 37.50 264 153 8 15896 16651 BACPLE_02533 [Bacteroides plebeius DSM 17135] ref|ZP_05280285.1| putative site-specific 36.88 263 155 7 15896 16651 DNA- methyltransferase [Bacteroides fragilis emb|CBL19545.1| DNA modification 35.06 251 154 6 15929 16654 methylase [Ruminococcus sp. SR1/5] ref|YP_003353511.1| phage DNA methylase 38.08 239 142 5 15944 16642 [Lactococcus lactis subsp. lactis KF147] ref|ZP_04822629.1| DNA (cytosine-5-)- 36.93 241 143 5 15944 16639 methyltransferase [Clostridium botulinum E1 str. ref|YP_672797.1| hypothetical protein 37.50 304 177 8 33414 32542 Meso_0228 [Mesorhizobium sp. BNC1] ref|ZP_03376876.1| putative helicase 43.40 235 131 4 12759 13457 [Salmonella enterica subsp. enterica serovar Typhi ref|YP_002502352.1| protein of unknown 45.20 177 96 2 21190 20663 function DUF847 [Methylobacterium nodulans ORS 2060] ref|ZP_04918174.1| DNA or RNA 31.29 163 108 2 12315 12791 helicases of superfamily II [Vibrio cholerae RC385] ref|ZP_04918174.1| DNA or RNA 40.91 110 65 1 11996 12325 helicases of superfamily II [Vibrio cholerae RC385] ref|YP_002826407.1| hypothetical protein 31.10 447 186 10 27287 26313 NGR_c18900 [Rhizobium sp. NGR234] ref|ZP_04680067.1| Hypothetical protein, 42.41 191 110 1 21202 20630 conserved [Ochrobactrum intermedium LMG 3301] ref|ZP_03528019.1| hypothetical protein 32.06 287 190 6 28647 27802 RetlC8_15010 [Rhizobium etli CIAT 894] ref|YP_613645.1| hypothetical protein 44.75 181 99 3 21202 20663 TM1040_1650 [Ruegeria sp. TM1040] ref|YP_613599.1| hypothetical protein 44.75 181 99 3 21202 20663 TM1040_1604 [Ruegeria sp. TM1040] ref|YP_612821.1| hypothetical protein 44.75 181 99 3 21202 20663 TM1040_0826 [Ruegeria sp. TM1040] ref|ZP_05854349.1| DNA (cytosine-5-)- 36.49 222 137 3 15989 16642 methyltransferase [Blautia hansenii DSM 20583] ref|YP_001592705.1| hypothetical protein 41.11 180 106 1 21202 20663 BCAN_A0869 [Brucella canis ATCC 23365] ref|ZP_05180771.1| hypothetical protein 38.50 200 115 2 21202 20627 Bru83_05374 [Brucella sp. 83/13] ref|ZP_05454244.1| hypothetical protein 40.78 179 106 1 21202 20666 Bmelb3E_11717 [Brucella melitensis bv. 3 str. ref|ZP_05175770.1| hypothetical protein 40.78 179 106 1 21202 20666 BcetM6_11506 [Brucella ceti M644/93/1] ref|YP_001258831.1| hypothetical protein 40.78 179 106 1 21202 20666 BOV_0848 [Brucella ovis ATCC 25840] ref|NP_540027.1| secretion activator 40.78 179 106 1 21202 20666 protein [Brucella melitensis 16M] ref|YP_001353888.1| hypothetical protein 27.92 462 328 16 29199 27829 mma_2198 [Janthinobacterium sp. Marseille] ref|YP_001353888.1| hypothetical protein 26.79 168 122 4 29634 29134 mma_2198 [Janthinobacterium sp. Marseille] ref|ZP_03370431.1| putative helicase 42.11 228 130 4 12780 13457 [Salmonella enterica subsp. enterica serovar Typhi ref|YP_001627531.1| hypothetical protein 40.22 179 107 1 21202 20666 BSUIS_A0894 [Brucella suis ATCC 23445] ref|ZP_05171770.1| hypothetical protein 40.22 179 107 1 21202 20666 BpinB_06732 [Brucella pinnipedialis B2/94] ref|ZP_04130502.1| DNA methylase N- 37.87 235 138 6 15956 16636 4/N-6 domain protein [Bacillus thuringiensis serovar ref|ZP_05331980.1| DNA methylase N- 32.64 242 159 4 15944 16657 4/N-6 domain- containing protein [Clostridium difficile ref|ZP_06792882.1| hypothetical protein 40.22 179 107 1 21202 20666 BAZG_01128 [Brucella sp. NVSL 07-0026] ref|YP_002826408.1| hypothetical protein 52.17 138 63 1 27706 27302 NGR_c18910 [Rhizobium sp. NGR234] ref|YP_455251.1| putative ATP- 29.83 181 123 2 12315 12845 dependent helicase [Sodalis glossinidius str. ‘morsitans’] ref|YP_455251.1| putative ATP- 39.25 107 65 1 11996 12316 dependent helicase [Sodalis glossinidius str. ‘morsitans’] emb|CAM75773.1| Helicase, C- 31.01 287 190 8 12333 13169 terminal:Type III restriction enzyme, res subunit:DEAD/DEAH emb|CAM75773.1| Helicase, C- 34.02 97 61 2 11996 12277 terminal:Type III restriction enzyme, res subunit:DEAD/DEAH ref|YP_419719.1| superfamily II 31.01 287 190 8 12333 13169 DNA/RNA helicase [Magnetospirillum magneticum AMB-1] ref|YP_419719.1| superfamily II 134.02 97 61 2 11996 12277 DNA/RNA helicase [Magnetospirillum magneticum AMB-1] ref|ZP_05181861.1| hypothetical protein 26.61 372 242 6 36810 35788 Bru83_11004 [Brucella sp. 83/13] ref|ZP_05181861.1| hypothetical protein 25.41 181 125 5 35625 35113 Bru83_11004 [Brucella sp. 83/13] ref|ZP_02082641.1| hypothetical protein 36.13 238 145 5 15944 16636 CLOBOL_00154 [Clostridium bolteae ATCC BAA-613] ref|YP_414410.1| secretion activator 45.14 175 96 1 21106 20582 protein, putative [Brucella melitensis biovar ref|ZP_03149730.1| phage uncharacterized 33.96 318 203 11 1378 446 protein [Geobacillus sp. G11MC16] ref|ZP_03149730.1| phage uncharacterized 35.11 131 84 2 2758 2369 protein [Geobacillus sp. G11MC16] ref|YP_001418062.1| hypothetical protein 41.76 170 95 3 21193 20696 Xaut_3175 [Xanthobacter autotrophicus Py2] ref|ZP_05155418.1| hypothetical protein 39.11 179 109 1 21202 20666 Babob3T_02779 [Brucella abortus bv. 3 str. Tulya] ref|NP_697992.1| secretion activator 44.57 175 97 1 21106 20582 protein, putative [Brucella suis 1330] ref|ZP_05895246.1| conserved hypothetical 41.07 168 99 1 21169 20666 protein [Brucella abortus bv. 9 str. C68] ref|ZP_03148199.1| phage uncharacterized 32.49 317 208 9 1378 446 protein [Geobacillus sp. G11MC16] ref|ZP_03148199.1| phage uncharacterized 35.88 131 83 2 2758 2369 protein [Geobacillus sp. G11MC16] ref|YP_001370913.1| hypothetical protein 39.55 177 107 1 21202 20672 Oant_2370 [Ochrobactrum anthropi ATCC 49188] ref|ZP_03053948.1| DNA methylase 36.47 255 146 8 15920 16636 [Bacillus pumilus ATCC 7061] ref|ZP_03053844.1| DNA methylase 35.39 243 152 4 15944 16657 [Bacillus pumilus ATCC 7061] ref|YP_001126919.1| terminase large 32.49 317 208 9 1378 446 subunit, putative [Geobacillus thermodenitrificans ref|YP_001126919.1| terminase large 34.35 131 85 2 2758 2369 subunit, putative [Geobacillus thermodenitrificans ref|ZP_05910454.1| helicase-related 39.23 260 155 7 12807 13577 protein [Vibrio parahaemolyticus AQ4037] ref|NP_761655.1| helicase-like protein 41.82 220 125 5 12807 13457 [Vibrio vulnificus CMCP6] ref|YP_001235617.1| phage uncharacterized 33.44 311 198 11 1378 473 protein [Acidiphilium cryptum JF-5] ref|YP_001235617.1| phage uncharacterized 34.96 123 80 1 2737 2369 protein [Acidiphilium cryptum JF-5] ref|YP_001294846.1| DNA methylase 34.96 246 154 5 15923 16642 [Burkholderia phage BcepNY3] ref|YP_001110197.1| DNA methylase N- 34.18 237 150 5 15944 16636 4/N-6 domain- containing protein [Burkholderia ref|ZP_05807828.1| protein of unknown 40.66 182 102 4 21187 20660 function DUF847 [Mesorhizobium opportunistum ref|ZP_03376875.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Typhi ref|ZP_03376875.1| putative helicase 30.16 126 84 2 12315 12680 [Salmonella enterica subsp. enterica serovar Typhi ref|YP_866814.1| type III restriction 29.66 290 196 8 12333 13178 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_866814.1| type III restriction 35.05 97 60 2 11996 12277 enzyme, res subunit [Magnetococcus sp. MC-1] ref|ZP_06243726.1| helicase domain 32.43 367 225 12 12324 13355 protein [Victivallis vadensis ATCC BAA- 548] ref|ZP_06243726.1| helicase domain 28.26 184 104 10 11996 12463 protein [Victivallis vadensis ATCC BAA- 548] ref|ZP_05620789.1| bifunctional DNA 23.15 691 505 21 5912 7906 primase/polymerase domain protein [Enhydrobacter ref|YP_745404.1| large terminase subunit 33.02 318 196 10 1375 473 [Granulibacter bethesdensis CGDNIH1] ref|YP_745404.1| large terminase subunit 35.06 174 110 5 2881 2369 [Granulibacter bethesdensis CGDNIH1] ref|NP_102244.1| hypothetical protein 36.73 226 136 4 26972 26316 mll0449 [Mesorhizobium loti MAFF303099] ref|NP_761654.1| superfamily II 41.82 110 64 1 11996 12325 DNA/RNA helicase [Vibrio vulnificus CMCP6] ref|NP_761654.1| superfamily II 24.84 153 111 2 12315 12761 DNA/RNA helicase [Vibrio vulnificus CMCP6] ref|NP_108621.1| hypothetical protein 41.94 186 102 4 21181 20642 mlr8547 [Mesorhizobium loti MAFF303099] ref|ZP_04567784.1| DNA methylase N- 35.08 248 149 5 15929 16636 4/N-6 domain- containing protein [Fusobacterium ref|ZP_04215575.1| Terminase large 31.33 316 201 12 1378 479 subunit [Bacillus cereus Rock4-2] ref|ZP_04215575.1| Terminase large 38.74 111 67 2 2671 2342 subunit [Bacillus cereus Rock4-2] ref|ZP_05181870.1| hypothetical protein 59.82 112 44 1 27634 27302 Bru83_11061 [Brucella sp. 83/13] ref|NP_108221.1| hypothetical protein 40.96 188 105 4 21187 20642 mlr8035 [Mesorhizobium loti MAFF303099] ref|ZP_05786522.1| secretion activator 45.10 153 83 2 21157 20702 protein [Silicibacter lacuscaerulensis ITI- 1157] ref|ZP_05082830.1| secretion activator 41.81 177 101 2 21202 20678 protein [Pseudovibrio sp. JE062] ref|NP_944318.1| gp10 [Burkholderia 35.17 236 147 5 15953 16642 phage Bcep1] ref|YP_003069080.1| putative helicase 32.17 286 186 10 12333 13166 domain protein, DEAD/DEAH motif [Methylobacterium ref|YP_003069080.1| putative helicase 32.73 110 71 2 11996 12316 domain protein, DEAD/DEAH motif [Methylobacterium emb|CBL08412.1| DNA modification 35.83 240 150 5 15944 16651 methylase [Roseburia intestinalis M50/1] ref|ZP_02038948.1| hypothetical protein 34.87 238 151 4 15944 16645 BACCAP_04595 [Bacteroides capillosus ATCC 29799] ref|ZP_02038963.1| hypothetical protein 34.87 238 151 4 15944 16645 BACCAP_04610 [Bacteroides capillosus ATCC 29799] ref|YP_001640282.1| helicase domain- 32.17 286 186 10 12333 13166 containing protein [Methylobacterium extorquens PA1] ref|YP_001640282.1| helicase domain- 32.73 110 71 2 11996 12316 containing protein [Methylobacterium extorquens PA1] ref|ZP_06361169.1| conserved hypothetical 33.64 220 146 1 30378 29719 protein [Rhodopseudomonas palustris DX-1] ref|ZP_05378025.1| protein of unknown 40.46 173 102 3 21199 20684 function DUF847 [Hyphomicrobium denitrificans ATCC ref|ZP_04100574.1| Large terminase 28.86 343 225 7 1444 473 subunit [Bacillus thuringiensis serovar berliner ATCC ref|ZP_04100574.1| Large terminase 36.11 108 68 2 2662 2342 subunit [Bacillus thuringiensis serovar berliner ATCC ref|ZP_03752697.1| hypothetical protein 35.42 240 151 5 15944 16651 ROSEINA2194_01101 [Roseburia inulinivorans DSM ref|YP_003309616.1| phage uncharacterized 29.05 327 211 10 1378 461 protein [Sebaldella termitidis ATCC 33386] ref|ZP_01550894.1| hypothetical protein 35.75 179 115 1 21199 20663 SIAM614_21537 [Stappia aggregata IAM 12614] ref|YP_001925629.1| helicase domain 30.99 313 201 12 12333 13226 protein [Methylobacterium populi BJ001] ref|YP_001925629.1| helicase domain 32.73 110 71 2 11996 12316 protein [Methylobacterium populi BJ001] ref|ZP_06537032.1| putative ATP- 42.73 110 63 1 11996 12325 dependent helicase [Salmonella enterica subsp. enterica ref|ZP_06537032.1| putative ATP- 32.29 96 61 2 12315 12590 dependent helicase [Salmonella enterica subsp. enterica ref|ZP_03356632.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Typhi ref|ZP_03356632.1| putative helicase 32.29 96 61 2 12315 12590 [Salmonella enterica subsp. enterica serovar Typhi ref|ZP_00741804.1| Large terminase 30.13 302 211 5 1378 473 subunit [Bacillus thuringiensis serovar israelensis ref|ZP_00741804.1| Large terminase 36.11 108 68 2 2662 2342 subunit [Bacillus thuringiensis serovar israelensis ref|ZP_00740989.1| Large terminase 28.57 343 226 8 1444 473 subunit [Bacillus thuringiensis serovar israelensis ref|ZP_00740989.1| Large terminase 37.04 108 67 2 2662 2342 subunit [Bacillus thuringiensis serovar israelensis ref|YP_001209644.1| hypothetical protein 39.41 170 102 2 21202 20696 DNO_0739 [Dichelobacter nodosus VCS1703A] ref|YP_003504938.1| uncharacterized phage 31.56 320 213 11 1378 437 protein [Denitrovibrio acetiphilus DSM 12809] ref|YP_003504938.1| uncharacterized phage 35.38 130 84 0 2731 2342 protein [Denitrovibrio acetiphilus DSM 12809] ref|YP_002421814.1| helicase domain 31.82 286 187 10 12333 13166 protein [Methylobacterium chloromethanicum CM4] ref|YP_002421814.1| helicase domain 31.82 110 72 2 11996 12316 protein [Methylobacterium chloromethanicum CM4] ref|YP_003550691.1| hypothetical protein 38.02 192 119 2 21259 20684 SAR116_0364 [alpha proteobacterium IMCC1322] ref|YP_001368768.1| HNH endonuclease 37.57 173 96 2 11490 11972 [Ochrobactrum anthropi ATCC 49188] emb|CBK98006.1| DNA modification 34.84 221 142 3 15989 16645 methylase [Faecalibacterium prausnitzii L2-6] ref|ZP_05375895.1| protein of unknown 40.46 173 102 3 21199 20684 function DUF847 [Hyphomicrobium denitrificans ATCC ref|ZP_05414485.1| DNA (cytosine-5-)- 32.81 253 153 6 15944 16651 methyltransferase [Bacteroides finegoldii DSM 17565] ref|ZP_02067759.1| hypothetical protein 33.60 253 151 8 15944 16651 BACOVA_04769 [Bacteroides ovatus ATCC 8483] ref|XP_001786642.1| predicted protein 39.25 186 108 5 1384 842 [Physcomitrella patens subsp. patens] ref|XP_001786642.1| predicted protein 29.91 117 76 3 2674 2342 [Physcomitrella patens subsp. patens] ref|ZP_04848440.1| conserved hypothetical 33.20 253 152 8 15944 16651 protein [Bacteroides sp. 1_1_6] ref|YP_002898939.1| putative HNH 37.35 166 101 1 11484 11972 endonuclease [Roseophage EE36P1] ref|ZP_03458269.1| hypothetical protein 33.60 253 151 8 15944 16651 BACEGG_01042 [Bacteroides eggerthii DSM 20697] ref|ZP_04194926.1| Terminase large 30.82 305 206 6 1378 479 subunit [Bacillus cereus AH676] ref|ZP_04194926.1| Terminase large 36.90 84 52 2 2617 2369 subunit [Bacillus cereus AH676] ref|ZP_05427405.1| DNA (cytosine-5-)- 34.65 228 136 6 15953 16597 methyltransferase [Eubacterium saphenum ATCC 49989] ref|ZP_05280292.1| DNA methylase N- 33.20 253 152 8 15944 16651 4/N-6 domain- containing protein [Bacteroides fragilis ref|ZP_03208876.1| hypothetical protein 33.60 253 151 8 15944 16651 BACPLE_02540 [Bacteroides plebeius DSM 17135] ref|ZP_02327823.1| hypothetical protein 34.18 237 148 6 15956 16642 Plarl_09255 [Paenibacillus larvae subsp. larvae ref|YP_498254.1| hypothetical protein 40.35 171 102 2 21190 20678 Saro_2985 [Novosphingobium aromaticivorans DSM ref|YP_917856.1| hypothetical protein 39.78 186 108 4 24268 23723 Pden_4094 [Paracoccus denitrificans PD1222] ref|YP_001552287.1| hypothetical protein 40.00 170 101 2 11472 11978 BA3_0018 [Thalassomonas phage BA3] ref|ZP_06744184.1| DEAD/DEAH box 30.22 278 182 9 12321 13118 helicase [Bacteroides vulgatus PC510] ref|ZP_06744184.1| DEAD/DEAH box 35.14 111 69 4 11996 12319 helicase [Bacteroides vulgatus PC510] ref|ZP_05257788.1| DNA methylase N- 33.86 254 150 9 15944 16651 4/N-6 domain- containing protein [Bacteroides sp. ref|ZP_01787476.1| hypothetical protein 29.25 318 208 10 1375 473 CGSHi22421_00957 [Haemophilus influenzae R3021] ref|ZP_01787476.1| hypothetical protein 32.52 123 72 2 2704 2369 CGSHi22421_00957 [Haemophilus influenzae R3021] ref|NP_203462.1| major virion structural 29.36 327 231 4 32466 31486 protein [Myxococcus phage Mx8] ref|NP_463999.1| hypothetical protein 34.83 201 127 3 16052 16642 lmo0470 [Listeria monocytogenes EGD- e] emb|CBA73542.1| conserved hypothetical 29.08 306 212 8 1375 473 phage protein [Arsenophonus nasoniae] emb|CBA73542.1| conserved hypothetical 31.71 123 73 2 2704 2369 phage protein [Arsenophonus nasoniae] ref|ZP_02494551.1| 3-phosphoglycerate 29.15 319 223 6 32457 31510 kinase [Burkholderia pseudomallei NCTC 13177] ref|YP_003187049.1| phage terminase large 31.72 309 202 8 1375 476 subunit TerL [Acetobacter pasteurianus IFO ref|YP_003187049.1| phage terminase large 34.13 167 109 2 2878 2381 subunit TerL [Acetobacter pasteurianus IFO ref|ZP_04725581.1| putative phage 40.00 165 91 2 11484 11954 associated protein [Neisseria gonorrhoeae FA19] ref|YP_002001290.1| putative phage 40.00 165 91 2 11484 11954 associated protein [Neisseria gonorrhoeae NCCP11945] ref|YP_001063342.1| 3-phosphoglycerate 29.15 319 223 6 32457 31510 kinase [Burkholderia pseudomallei 668] ref|ZP_01788573.1| hypothetical protein 28.62 318 210 10 1375 473 CGSHi3655_09046 [Haemophilus influenzae 3655] ref|ZP_01788573.1| hypothetical protein 33.06 124 71 2 2704 2369 CGSHi3655_09046 [Haemophilus influenzae 3655] ref|ZP_03009861.1| hypothetical protein 33.20 253 152 8 15944 16651 BACCOP_01723 [Bacteroides coprocola DSM 17136] ref|NP_203466.1| hypothetical protein 26.61 387 274 13 28872 27742 Mx8p52 [Myxococcus phage Mx8] ref|ZP_05521263.1| terminase large 30.87 311 185 9 1375 533 subunit, putative [Streptomyces hygroscopicus ATCC ref|ZP_05521263.1| terminase large 31.36 118 79 2 2737 2390 subunit, putative [Streptomyces hygroscopicus ATCC ref|YP_002117646.1| p088 [Rhizobium 31.30 262 171 8 12324 13082 phage 16-3] ref|YP_002117646.1| p088 [Rhizobium 31.96 97 63 2 11996 12277 phage 16-3] ref|ZP_05332310.1| putative site-specific 33.60 247 150 6 15944 16642 DNA- methyltransferase [Clostridium difficile ref|NP_958672.1| Bbp2 [Bordetella 40.24 169 101 2 21193 20687 phage BPP-1] ref|ZP_04740538.1| putative phage 39.39 165 92 2 11484 11954 associated protein [Neisseria gonorrhoeae SK-93-1035] ref|ZP_04440303.1| probable site-specific 31.43 245 159 6 15962 16669 DNA- methyltransferase [Lactobacillus rhamnosus ref|ZP_03707983.1| hypothetical protein 32.35 238 157 4 15944 16645 CLOSTMETH_02741 [Clostridium methylpentosum DSM ref|ZP_04719195.1| putative phage 32.40 321 210 10 1381 440 associated protein [Neisseria gonorrhoeae 35/02] ref|ZP_04719195.1| putative phage 29.41 119 83 2 2743 2390 associated protein [Neisseria gonorrhoeae 35/02] ref|YP_002117655.1| p097 [Rhizobium 35.80 243 156 9 15917 16645 phage 16-3] ref|YP_001693301.1| DNA methylase 32.08 240 155 4 15944 16639 [Clostridium botulinum B1 str. Okra] ref|NP_471068.1| hypothetical protein 28.94 349 210 12 1378 446 lin1732 [Listeria innocua Clip11262] ref|NP_471068.1| hypothetical protein 28.65 185 131 3 2893 2342 lin1732 [Listeria innocua Clip11262] ref|ZP_02032066.1| hypothetical protein 29.37 269 178 8 12324 13094 PARMER_02074 [Parabacteroides merdae ATCC 43184] ref|ZP_02032066.1| hypothetical protein 36.94 111 67 4 11993 12316 PARMER_02074 [Parabacteroides merdae ATCC 43184] ref|YP_003344808.1| putative terminase 27.99 318 212 11 1375 473 large subunit TerL [Aggregatibacter phage S1249] ref|YP_003344808.1| putative terminase 31.11 135 78 3 2728 2369 large subunit TerL [Aggregatibacter phage S1249] ref|ZP_04720728.1| putative phage 32.40 321 210 10 1381 440 associated protein [Neisseria gonorrhoeae DGI18] ref|ZP_04720728.1| putative phage 29.41 119 83 2 2743 2390 associated protein [Neisseria gonorrhoeae DGI18] ref|ZP_03643400.1| hypothetical protein 31.10 254 159 7 15944 16657 BACCOPRO_01768 [Bacteroides coprophilus DSM 18228] ref|YP_001715839.1| DNA methylase 32.24 245 153 6 15944 16639 [Clostridium botulinum A3 str. Loch Maree] ref|NP_852753.1| putative terminase 27.99 318 212 11 1375 473 large subunit TerL [Haemophilus phage Aaphi23] ref|NP_852753.1| putative terminase 30.37 135 79 3 2728 2369 large subunit TerL [Haemophilus phage Aaphi23] ref|ZP_06643501.1| phage associated 38.79 165 93 2 11484 11954 protein [Neisseria gonorrhoeae F62] emb|CBL41024.1| DNA modification 33.61 238 154 5 15944 16645 methylase [Clostridiales sp. SS3/4] ref|YP_002002065.1| putative phage 32.09 321 211 10 1381 440 associated protein [Neisseria gonorrhoeae NCCP11945] ref|YP_002002065.1| putative phage 29.41 119 83 2 2743 2390 associated protein [Neisseria gonorrhoeae NCCP11945] ref|YP_001875859.1| DNA methylase N- 34.55 246 155 10 15917 16636 4/N-6 domain- containing protein [Elusimicrobium minutum ref|YP_208181.1| putative phage 38.79 165 93 2 11484 11954 associated protein [Neisseria gonorrhoeae FA 1090] ref|YP_207645.1| putative phage 32.09 321 211 10 1381 440 associated protein [Neisseria gonorrhoeae FA 1090] ref|YP_207645.1| putative phage 29.41 119 83 2 2743 2390 associated protein [Neisseria gonorrhoeae FA 1090] ref|YP_001302249.1| hypothetical protein 29.63 270 178 9 12324 13097 BDI_0858 [Parabacteroides distasonis ATCC 8503] ref|YP_001302249.1| hypothetical protein 40.00 90 51 3 11993 12253 BDI_0858 [Parabacteroides distasonis ATCC 8503] ref|YP_001285555.1| EndY [Enterobacteria 49.18 122 60 1 11610 11969 phage TLS] ref|ZP_06663130.1| endonuclease 40.24 169 99 3 11472 11972 [Escherichia coli B088] ref|ZP_04757897.1| putative phage protein 31.78 321 212 10 1381 440 [Neisseria flavescens SK114] ref|ZP_04757897.1| putative phage protein 28.81 118 84 1 2743 2390 [Neisseria flavescens SK114] ref|ZP_06628270.1| putative terminase, 30.06 336 211 11 1378 443 large subunit [Enterococcus faecalis R712] ref|ZP_06628270.1| putative terminase, 29.23 130 86 4 2740 2369 large subunit [Enterococcus faecalis R712] ref|ZP_03983304.1| phage possible protein 29.79 339 211 12 1378 443 [Enterococcus faecalis HH22] ref|ZP_03983304.1| phage possible protein 29.23 130 86 4 2740 2369 [Enterococcus faecalis HH22] gb|ABD63727.1| putative terminase 29.91 331 205 13 1384 473 large subunit [Lactococcus phage ul36.k1t1] gb|ABD63727.1| putative terminase 28.46 123 87 2 2734 2369 large subunit [Lactococcus phage ul36.k1t1] ref|NP_815176.1| terminase, large 29.23 349 223 12 1378 404 subunit, putative [Enterococcus faecalis V583] ref|NP_815176.1| terminase, large 29.23 130 86 4 2740 2369 subunit, putative [Enterococcus faecalis V583] ref|NP_102245.1| hypothetical protein 49.11 112 56 1 27634 27302 mll0450 [Mesorhizobium loti MAFF303099] ref|ZP_05579649.1| conserved hypothetical 29.76 336 212 11 1378 443 protein [Enterococcus faecalis Fly1] ref|ZP_05579649.1| conserved hypothetical 29.23 130 86 4 2740 2369 protein [Enterococcus faecalis Fly1] ref|ZP_05854196.1| DNA (cytosine-5-)- 33.19 238 155 5 15944 16645 methyltransferase [Blautia hansenii DSM 20583] ref|YP_002328249.1| predicted 46.34 123 64 1 11610 11972 endonuclease [Escherichia coli O127:H6 str. E2348/69] emb|CAJ28416.1| terminase large subunit 30.48 315 205 10 1375 473 [Phage PY100] ref|YP_003169232.1| protein of unknown 36.76 185 107 2 21199 20675 function DUF847 [Candidatus Accumulibacter ref|YP_003325139.1| phage uncharacterized 28.44 320 211 9 1378 473 protein [Xylanimonas cellulosilytica DSM 15894] ref|YP_003325139.1| phage uncharacterized 29.06 117 81 3 2686 2342 protein [Xylanimonas cellulosilytica DSM 15894] emb|CBK77887.1| DNA modification 33.61 238 154 5 15944 16645 methylase [Clostridium saccharolyticum-like K10] gb|ABP57294.1| hypothetical protein 31.05 248 159 5 15944 16651 bst021 [Bacteroides uniformis] ref|YP_001562680.1| hypothetical protein 38.27 162 100 2 21190 20705 Daci_1652 [Delftia acidovorans SPH-1] ref|ZP_05257320.1| conserved hypothetical 30.48 269 175 8 12324 13094 protein [Bacteroides sp. 4_3_47FAA] ref|ZP_05257320.1| conserved hypothetical 34.82 112 68 5 11996 12316 protein [Bacteroides sp. 4_3_47FAA] ref|ZP_06349823.1| protein of unknown 37.36 182 113 3 21193 20651 function DUF847 [Rhodomicrobium vannielii ATCC ref|ZP_05918562.1| conserved hypothetical 27.78 342 228 9 1438 470 protein [Prevotella sp. oral taxon 472 str. ref|ZP_05918562.1| conserved hypothetical 35.48 93 59 1 2728 2453 protein [Prevotella sp. oral taxon 472 str. ref|YP_003041966.1| hypothetical protein 35.59 222 119 9 10760 11353 PAU_03136 [Photorhabdus asymbiotica] ref|ZP_06090627.1| conserved hypothetical 29.35 276 176 9 12324 13094 protein [Bacteroides sp. 3_1_33FAA] ref|ZP_06090627.1| conserved hypothetical 35.45 110 68 4 11996 12316 protein [Bacteroides sp. 3_1_33FAA] emb|CBK98101.1| DNA modification 33.03 221 146 4 15989 16645 methylase [Faecalibacterium prausnitzii L2-6] ref|YP_003065547.1| hypothetical protein 29.67 273 186 5 28701 27901 CLIBASIA_05180 [Candidatus Liberibacter asiaticus ref|YP_453589.1| HNH endonuclease 39.61 154 91 3 11475 11930 family protein [Xanthomonas phage OP1] ref|ZP_05907433.1| helicase-related 40.91 110 65 1 11996 12325 protein [Vibrio parahaemolyticus Peru-466] ref|ZP_05907433.1| helicase-related 28.05 82 55 2 12315 12548 protein [Vibrio parahaemolyticus Peru-466] ref|YP_001770241.1| helicase domain- 32.13 249 161 8 12333 13055 containing protein [Methylobacterium sp. 4-46] ref|YP_001770241.1| helicase domain- 31.63 98 55 5 11996 12253 containing protein [Methylobacterium sp. 4-46] ref|ZP_06782195.1| hypothetical protein 39.76 166 100 2 21202 20705 A60131_06220 [Acinetobacter sp. 6013113] ref|YP_001327487.1| hypothetical protein 36.87 198 120 6 26900 26322 Smed_1817 [Sinorhizobium medicae WSM419] ref|YP_001327487.1| hypothetical protein 45.61 114 62 0 27278 26937 Smed_1817 [Sinorhizobium medicae WSM419] ref|ZP_03223900.1| DNA methylase 29.19 298 148 8 15941 16645 [Salmonella enterica subsp. enterica serovar 4,[5],12:i:— ref|YP_001599091.1| hypothetical protein 36.75 166 105 2 21202 20705 NMCC_0954 [Neisseria meningitidis 053442] ref|YP_001754215.1| helicase domain- 31.74 293 185 11 12333 13166 containing protein [Methylobacterium radiotolerans JCM ref|YP_001754215.1| helicase domain- 32.88 73 46 2 12065 12274 containing protein [Methylobacterium radiotolerans JCM ref|YP_001742088.1| putative endonuclease 44.53 128 69 1 11592 11969 protein [Salmonella phage E1] ref|ZP_02494544.1| hypothetical protein 29.13 381 212 14 27284 26316 BpseN_34235 [Burkholderia pseudomallei NCTC 13177] ref|YP_468632.1| hypothetical protein 28.12 320 229 5 32466 31510 RHE_CH01097 [Rhizobium etli CFN 42] ref|YP_419721.1| hypothetical protein 24.62 589 413 21 6452 8125 amb0358 [Magnetospirillum magneticum AMB-1] ref|ZP_01261287.1| helicase-related 41.82 110 64 1 11996 12325 protein [Vibrio alginolyticus 12G01] ref|ZP_01261287.1| helicase-related 29.49 78 51 2 12315 12536 protein [Vibrio alginolyticus 12G01] ref|YP_001063336.1| hypothetical protein 29.13 381 212 14 27284 26316 BURPS668_A2342 [Burkholderia pseudomallei 668] ref|YP_769512.1| hypothetical protein 28.44 320 228 5 32466 31510 RL3934 [Rhizobium leguminosarum bv. viciae 3841] ref|ZP_06787471.1| hypothetical protein 29.32 307 212 10 1381 476 A6014_13049 [Acinetobacter sp. 6014059] ref|ZP_06787471.1| hypothetical protein 27.42 124 89 1 2731 2363 A6014_13049 [Acinetobacter sp. 6014059] ref|ZP_05756780.1| DNA methylase N- 30.67 238 142 7 15953 16597 4/N-6 domain- containing protein [Bacteroides sp. D2] emb|CBA06915.1| conserved hypothetical 36.14 166 106 2 21202 20705 protein [Neisseria meningitidis alpha153] ref|YP_002320044.1| hypothetical protein 29.32 307 212 10 1381 476 AB57_2704 [Acinetobacter baumannii AB0057] ref|YP_002320044.1| hypothetical protein 27.42 124 89 1 2731 2363 AB57_2704 [Acinetobacter baumannii AB0057] ref|NP_858997.1| endonuclease of the 38.56 153 92 3 11475 11927 HNH family with predicted DNA- binding module in the ref|NP_274047.1| hypothetical protein 36.14 166 106 2 21202 20705 NMB1012 [Neisseria meningitidis MC58] ref|YP_001565093.1| hypothetical protein 39.51 162 98 4 21193 20708 Daci_4077 [Delftia acidovorans SPH-1] ref|ZP_02426493.1| hypothetical protein 27.88 312 215 8 1375 470 ALIPUT_02660 [Alistipes putredinis DSM 17216] ref|ZP_02426493.1| hypothetical protein 38.78 98 59 1 2743 2453 ALIPUT_02660 [Alistipes putredinis DSM 17216] ref|YP_003279035.1| hypothetical protein 33.47 248 158 9 24457 23735 CtCNB1_2993 [Comamonas testosteroni CNB-2] gb|ABO12457.2| hypothetical protein 28.99 307 213 10 1381 476 putative phage associated protein [Acinetobacter gb|ABO12457.2| hypothetical protein 27.54 138 99 2 2731 2321 putative phage associated protein [Acinetobacter ref|YP_001085059.1| putative phage 28.99 307 213 10 1381 476 associated protein [Acinetobacter baumannii ATCC ref|YP_001085059.1| putative phage 27.54 138 99 2 2731 2321 associated protein [Acinetobacter baumannii ATCC ref|ZP_03375127.1| putative helicase 32.32 164 107 2 12315 12794 [Salmonella enterica subsp. enterica serovar Typhi ref|ZP_03375127.1| putative helicase 34.09 44 29 0 12194 12325 [Salmonella enterica subsp. enterica serovar Typhi ref|ZP_06788596.1| hypothetical protein 29.51 305 212 10 1381 476 A6014_18731 [Acinetobacter sp. 6014059] ref|ZP_06788596.1| hypothetical protein 28.26 138 98 2 2731 2321 A6014_18731 [Acinetobacter sp. 6014059] ref|YP_001847402.1| hypothetical protein 29.51 305 212 10 1381 476 ACICU_02743 [Acinetobacter baumannii ACICU] ref|YP_001847402.1| hypothetical protein 28.26 138 98 2 2731 2321 ACICU_02743 [Acinetobacter baumannii ACICU] ref|YP_975058.1| hypothetical protein 35.54 166 107 2 21202 20705 NMC1002 [Neisseria meningitidis FAM18] ref|YP_001285722.1| p55.1 [Xanthomonas 38.56 153 92 3 11475 11927 phage Xop411] emb|CBL04730.1| DNA modification 31.47 232 146 6 15941 16597 methylase [Gordonibacter pamelaeae 7-10-1-bT] ref|YP_003257431.1| hypothetical protein 38.22 191 111 5 1375 824 pZL12-67 [Streptomyces sp. ZL12] ref|YP_003923.1| putative ATP- 30.31 353 215 13 12522 13487 dependent helicase [Enterobacteria phage T1] ref|YP_003923.1| putative ATP- 31.37 102 70 1 12002 12307 dependent helicase [Enterobacteria phage T1] ref|ZP_06097802.1| conserved hypothetical 33.33 297 107 6 27287 26670 protein [Brucella sp. 83/13] emb|CBA05974.1| conserved hypothetical 35.54 166 107 2 21202 20705 protein [Neisseria meningitidis serogroup W135] emb|CAM75771.1| primase 24.61 512 359 17 6452 7906 [Magnetospirillum gryphiswaldense MSR-1] pdb|2IS5|A Chain A, Crystal 36.42 162 103 2 21190 20705 Structure Of 3 Residues Truncated Version Of Protein pdb|2IKB|A Chain A, Crystal 36.42 162 103 2 21190 20705 Structure Of A Protein Of Unknown Function Nmb1012 ref|XP_002336241.1| predicted protein 39.13 161 98 3 21190 20708 [Populus trichocarpa] ref|YP_002440151.1| hypothetical protein 35.06 174 101 4 11484 11969 PLES_25511 [Pseudomonas aeruginosa LESB58] ref|NP_859005.1| endonuclease of the 37.91 153 93 3 11475 11927 HNH family with predicted DNA- binding module at ref|YP_002330023.1| predicted HNH 38.78 147 86 2 11466 11894 endonuclease [Escherichia coli O127:H6 str. E2348/69] ref|YP_001629579.1| hypothetical protein 27.68 336 236 11 1459 473 Bpet0976 [Bordetella petrii DSM 12804] ref|YP_001629579.1| hypothetical protein 30.77 117 80 1 2737 2390 Bpet0976 [Bordetella petrii DSM 12804] ref|ZP_05360494.1| secretion activator 35.54 166 103 2 21190 20705 protein [Acinetobacter radioresistens SK82] ref|NP_858964.1| endonuclease of the 36.84 152 95 2 11475 11927 HNH family [Xanthomonas phage Xp10] ref|YP_003060760.1| protein of unknown 33.33 174 107 5 21190 20696 function DUF847 [Hirschia baltica ATCC 49814] ref|YP_001742082.1| putative ATP- 27.16 416 273 13 12423 13580 dependent helicase [Salmonella phage E1] ref|YP_001742082.1| putative ATP- 33.71 89 59 2 12059 12325 dependent helicase [Salmonella phage E1] ref|YP_917855.1| hypothetical protein 33.88 245 156 8 23153 22437 Pden_4093 [Paracoccus denitrificans PD1222] gb|ADA72691.1| HNH endonuclease 46.02 113 59 1 11640 11972 [Shigella flexneri 2002017] ref|YP_001467758.1| chaperone and heat 27.65 311 218 9 1375 464 shock protein 70 [Campylobacter concisus 13826] ref|YP_001467758.1| chaperone and heat 29.61 179 115 6 2881 2378 shock protein 70 [Campylobacter concisus 13826] ref|ZP_05431357.1| HNH endonuclease 46.02 113 59 1 11640 11972 [Shigella sp. D9] ref|ZP_04945757.1| hypothetical protein 41.67 156 88 4 11484 11942 BDAG_01666 [Burkholderia dolosa AUO158] emb|CAX50201.1| conserved hypothetical 34.94 166 108 2 21202 20705 protein [Neisseria meningitidis 8013] ref|YP_002438405.1| EndY [Pseudomonas 37.12 132 83 0 11577 11972 aeruginosa LESB58] ref|YP_001789610.1| hypothetical protein 36.20 163 103 2 21181 20696 Lcho_0570 [Leptothrix cholodnii SP-6] ref|YP_001300123.1| putative ATP- 28.29 258 175 10 12321 13064 dependent helicase [Bacteroides vulgatus ATCC 8482] ref|YP_001300123.1| putative ATP- 36.84 114 70 4 11984 12319 dependent helicase [Bacteroides vulgatus ATCC 8482] emb|CBK86224.1| AP2 domain. 39.47 152 91 2 11490 11942 [Enterobacter cloacae NCTC 9394] ref|ZP_05435815.1| hypothetical protein 38.27 162 99 4 11490 11972 E4_01140 [Escherichia sp. 4_1_40B] ref|YP_001285711.1| p42.1 [Xanthomonas 37.91 153 93 3 11475 11927 phage Xop411] ref|ZP_05055011.1| hypothetical protein 50.00 104 52 1 3302 2991 OA307_933 [Octadecabacter antarcticus 307] ref|ZP_04978507.1| hypothetical 35.12 168 109 2 21190 20687 bacteriophage protein [Mannheimia haemolytica PHL213] ref|YP_865630.1| hypothetical protein 27.85 316 228 3 32457 31510 Mmc1_1716 [Magnetococcus sp. MC-1] ref|NP_102247.1| hypothetical protein 30.87 230 158 2 30378 29692 mll0453 [Mesorhizobium loti MAFF303099] ref|YP_001992359.1| protein of unknown 34.36 195 115 7 21202 20657 function DUF847 [Rhodopseudomonas palustris TIE-1] ref|YP_001353886.1| hypothetical protein 33.33 276 163 9 27278 26514 mma_2196 [Janthinobacterium sp. Marseille] ref|YP_003937.1| putative endonuclease 37.66 154 92 5 11520 11969 [Enterobacteria phage T1] ref|YP_453670.1| putative phage helicase 25.94 239 171 6 12354 13052 [Xanthomonas phage OP2] ref|YP_453670.1| putative phage helicase 32.20 118 73 4 11984 12316 [Xanthomonas phage OP2] ref|ZP_02682965.1| HNH endonuclease 35.67 171 108 3 11466 11972 family protein [Salmonella enterica subsp. enterica ref|YP_002280254.1| hypothetical protein 29.46 258 182 3 32283 31510 Rleg2_0732 [Rhizobium leguminosarum bv. trifolii ref|ZP_06361170.1| conserved hypothetical 29.67 246 151 6 31062 30391 protein [Rhodopseudomonas palustris DX-1] ref|ZP_06019578.1| conserved hypothetical 27.35 373 238 15 1492 473 protein [Lactobacillus crispatus MV-3A-US] ref|ZP_05361197.1| conserved hypothetical 30.15 325 219 13 1378 428 protein [Acinetobacter radioresistens SK82] ref|ZP_05361197.1| conserved hypothetical 26.96 115 83 1 2731 2390 protein [Acinetobacter radioresistens SK82] ref|YP_001595442.1| putative HNH 36.65 161 102 2 11484 11966 endonuclease [Enterobacteria phage phiEcoM-GJ1] ref|YP_087300.1| hypothetical protein 33.13 163 109 2 21190 20702 MS0108 [Mannheimia succiniciproducens MBEL55E] ref|YP_001784196.1| hypothetical protein 33.96 212 126 5 10760 11353 HSM_0864 [Haemophilus somnus 2336] ref|ZP_05575019.1| DEAD box family 28.06 253 179 8 12327 13076 helicase [Enterococcus faecalis E1Sol] ref|ZP_05575019.1| DEAD box family 30.39 102 70 2 11996 12298 helicase [Enterococcus faecalis E1Sol] ref|ZP_06222047.1| hypothetical protein 37.89 161 100 2 21184 20702 HAINFHK1212_1942 [Haemophilus influenzae HK1212] ref|ZP_06222396.1| hypothetical protein 37.74 159 99 2 21178 20702 HAINFHK1212_0139 [Haemophilus influenzae HK1212] ref|YP_002363335.1| protein of unknown 34.66 176 114 3 21190 20666 function DUF847 [Methylocella silvestris BL2] ref|YP_002287849.1| secretion activator 33.33 180 119 3 21163 20627 protein [Oligotropha carboxidovorans OM5] ref|YP_001603102.1| DNA methylase N- 30.74 231 151 4 15941 16606 4/N-6 domain- containing protein [Gluconacetobacter ref|YP_453616.1| HNH endonuclease 35.53 152 97 3 11475 11927 family protein [Xanthomonas phage OP1] ref|ZP_06016778.1| conserved hypothetical 43.20 125 69 2 11610 11978 protein [Klebsiella pneumoniae subsp. ref|YP_001285569.1| EndZ [Enterobacteria 39.57 139 82 1 11562 11972 phage TLS] ref|YP_001285548.1| HelA [Enterobacteria 27.33 439 279 19 12414 13610 phage TLS] ref|YP_001285548.1| HelA [Enterobacteria 30.93 97 67 1 12005 12295 phage TLS] ref|NP_888770.1| hypothetical protein 40.00 140 82 4 11490 11903 BB2226 [Bordetella bronchiseptica RB50] ref|XP_711763.1| hypothetical protein 28.35 261 176 8 12303 13052 CaO19.10315 [Candida albicans SC5314] ref|XP_711763.1| hypothetical protein 32.35 68 46 1 11996 12199 CaO19.10315 [Candida albicans SC5314] ref|YP_398984.1| putative HNH 37.01 154 94 2 11517 11969 endonuclease [Enterobacteria phage RTP] ref|YP_001344507.1| hypothetical protein 35.98 214 121 7 10760 11353 Asuc_1210 [Actinobacillus succinogenes 130Z] ref|NP_102251.1| hypothetical protein 25.09 275 201 6 33396 32587 mll0458 [Mesorhizobium loti MAFF303099] ref|ZP_04464409.1| hypothetical protein 37.82 156 97 2 21169 20702 CGSHi6P18H1_08105 [Haemophilus influenzae 6P18H1] ref|ZP_05122973.1| DNA methylase 32.36 275 170 8 15908 16684 [Rhodobacteraceae bacterium KLH11] emb|CAJ28486.1| NTP dependent 28.35 388 242 19 12522 13577 helicase [Phage PY100] ref|ZP_06294764.1| protein of unknown 33.13 163 109 3 21193 20705 function DUF847 [Burkholderia sp. CCGE1001] ref|ZP_06222476.1| poly(A) polymerase 36.36 165 105 2 21196 20702 [Haemophilus influenzae HK1212] ref|ZP_06222539.1| hypothetical protein 36.65 161 102 2 21184 20702 HAINFHK1212_1520 [Haemophilus influenzae HK1212] gb|EEQ42459.1| conserved hypothetical 26.82 261 180 8 12303 13052 protein [Candida albicans WO-1] gb|EEQ42459.1| conserved hypothetical 32.35 68 46 1 11996 12199 protein [Candida albicans WO-1] ref|ZP_06288708.1| DEAD/DEAH box 25.77 291 196 12 12321 13133 helicase [Prevotella timonensis CRIS 5C- B1] ref|ZP_06288708.1| DEAD/DEAH box 34.21 114 73 4 11984 12319 helicase [Prevotella timonensis CRIS 5C- B1] ref|YP_001565108.1| pathogenesis-related 35.54 166 94 5 11490 11948 transcriptional factor and ERF protein [Delftia ref|YP_575655.1| HNH endonuclease 40.65 123 71 1 11610 11972 [Nitrobacter hamburgensis X14] ref|NP_881902.1| hypothetical protein 39.29 140 83 4 11490 11903 BP3370 [Bordetella pertussis Tohama I] ref|ZP_06222379.1| hypothetical protein 37.82 156 97 2 21169 20702 HAINFHK1212_1590 [Haemophilus influenzae HK1212] ref|ZP_06223216.1| hypothetical protein 36.81 163 103 2 21190 20702 HAINFHK1212_0338 [Haemophilus influenzae HK1212] gb|EEQ42458.1| conserved hypothetical 26.64 259 183 7 12297 13052 protein [Candida albicans WO-1] gb|EEQ42458.1| conserved hypothetical 35.29 68 44 1 11996 12199 protein [Candida albicans WO-1] ref|YP_003608210.1| protein of unknown 32.52 163 110 3 21193 20705 function DUF847 [Burkholderia sp. CCGE1002] ref|ZP_05783661.1| conserved hypothetical 25.09 558 391 23 6551 8143 protein [Citreicella sp. SE45] ref|XP_711764.1| hypothetical protein 26.64 259 183 7 12297 13052 CaO19.10316 [Candida albicans SC5314] ref|XP_711764.1| hypothetical protein 35.29 68 44 1 11996 12199 CaO19.10316 [Candida albicans SC5314] gb|ADD96376.1| hypothetical protein 30.67 163 111 2 11451 11933 yberc0001_14950 [uncultured organism ref|YP_003376236.1| hypothetical protein of 35.16 182 103 6 21193 20693 unknown function duf847 [Xanthomonas ref|ZP_06221712.1| hypothetical protein 38.56 153 94 2 21160 20702 HAINFHK1212_1133 [Haemophilus influenzae HK1212] ref|ZP_06221842.1| hypothetical protein 38.56 153 94 2 21160 20702 HAINFHK1212_2061 [Haemophilus influenzae HK1212] ref|ZP_06222749.1| DNA topoisomerase 38.56 153 94 2 21160 20702 III [Haemophilus influenzae HK1212] ref|ZP_06222012.1| hypothetical protein 38.56 153 94 2 21160 20702 HAINFHK1212_1041 [Haemophilus influenzae HK1212] ref|ZP_06222819.1| hypothetical protein 38.56 153 94 2 21160 20702 HAINFHK1212_1706 [Haemophilus influenzae HK1212] ref|ZP_05375782.1| protein of unknown 33.17 199 126 5 21199 20624 function DUF847 [Hyphomicrobium denitrificans ATCC ref|ZP_03995517.1| phage protein 27.75 364 225 15 1450 473 [Lactobacillus crispatus JV-V01] ref|ZP_04977471.1| hypothetical protein 33.53 170 112 3 21193 20687 MHA_0919 [Mannheimia haemolytica PHL213] ref|ZP_04898487.1| putative conserved 27.15 372 248 12 1522 476 hypothetical protein [Burkholderia pseudomallei ref|ZP_04898487.1| putative conserved 26.92 130 91 2 2731 2354 hypothetical protein [Burkholderia pseudomallei ref|YP_001285701.2| p31.1 [Xanthomonas 36.99 146 89 3 11499 11927 phage Xop411] ref|YP_003550710.1| Microcystin-dependent 35.96 203 128 7 21955 21353 protein-like protein [alpha proteobacterium ref|YP_002922896.1| putative HNH 35.80 162 103 2 11490 11972 endonuclease [Enterobacteria phage WV8] ref|YP_880745.1| gp2 protein 27.60 279 185 9 1561 776 [Mycobacterium avium 104] ref|YP_880745.1| gp2 protein 29.69 128 89 2 2722 2342 [Mycobacterium avium 104] ref|ZP_00782397.1| helicase, putative 25.10 259 185 7 12327 13076 [Streptococcus agalactiae H36B] ref|ZP_00782397.1| helicase, putative 30.39 102 70 2 11996 12298 [Streptococcus agalactiae H36B] ref|ZP_06019826.1| conserved hypothetical 25.91 359 233 14 1450 473 protein [Lactobacillus crispatus MV-3A-US] ref|ZP_02883093.1| protein of unknown 33.13 163 109 3 21193 20705 function DUF847 [Burkholderia graminis C4D1M] ref|YP_001072155.1| hypothetical protein 27.24 279 186 9 1561 776 Mjls_3888 [Mycobacterium sp. JLS] ref|YP_001072155.1| hypothetical protein 29.69 128 89 2 2722 2342 Mjls_3888 [Mycobacterium sp. JLS] ref|YP_001006557.1| hypothetical protein 34.52 168 102 3 11466 11945 YE2335 [Yersinia enterocolitica subsp. ref|NP_944978.1| Putative HNH 35.85 159 100 3 11502 11972 endonuclease [Enterobacteria phage Felix 01] ref|YP_600161.1| DNA/RNA helicase 25.19 266 190 7 12306 13076 [Streptococcus phage 2096.1] ref|YP_600161.1| DNA/RNA helicase 31.37 102 69 2 11996 12298 [Streptococcus phage 2096.1] ref|NP_268909.1| DEAD box family 25.19 266 190 7 12306 13076 helicase [Streptococcus phage 370.1] ref|NP_268909.1| DEAD box family 31.37 102 69 2 11996 12298 helicase [Streptococcus phage 370.1] gb|ADF83450.1| putative DNA 29.18 281 152 11 15944 16645 methylase [Lactobacillus phage LBR48] ref|XP_002417354.1| conserved hypothetical 26.64 259 183 7 12297 13052 protein [Candida dubliniensis CD36] ref|XP_002417354.1| conserved hypothetical 33.82 68 45 1 11996 12199 protein [Candida dubliniensis CD36] ref|ZP_06606319.1| terminase large subunit 26.99 326 214 13 1378 473 [Aeromicrobium marinum DSM 15272] ref|YP_003084146.1| large terminase subunit 24.85 330 231 8 1375 437 [Cyanophage PSS2] ref|YP_002911899.1| DNA methylase N- 29.10 244 162 9 15947 16645 4/N-6 domain protein [Burkholderia glumae BGR1] ref|YP_001887786.1| protein of unknown 34.36 163 107 4 21193 20705 function DUF847 [Burkholderia phytofirmans PsJN] ref|YP_554806.1| hypothetical protein 33.13 163 109 3 21193 20705 Bxe_B0491 [Burkholderia xenovorans LB400] gb|EFG74825.1| gp2 protein 27.24 279 186 9 1561 776 [Mycobacterium parascrofulaceum ATCC BAA-614] gb|EFG74825.1| gp2 protein 29.69 128 89 2 2722 2342 [Mycobacterium parascrofulaceum ATCC BAA-614] ref|YP_001469624.1| HNH endonuclease 34.81 158 102 3 11490 11960 [Xanthomonas phage Xop411] ref|YP_001239849.1| hypothetical protein 30.00 190 127 3 21163 20612 BBta_3868 [Bradyrhizobium sp. BTAi1] emb|CBK86236.1| AP2 domain. 37.58 149 91 3 11475 11915 [Enterobacter cloacae NCTC 9394] ref|ZP_06469271.1| conserved hypothetical 34.36 163 107 4 21193 20705 protein [Burkholderia sp. CCGE1003] ref|ZP_06089323.1| LOW QUALITY 37.80 164 94 4 16184 16651 PROTEIN: conserved hypothetical protein [Bacteroides sp. ref|ZP_04752828.1| hypothetical 32.94 170 113 3 21193 20687 bacteriophage protein [Actinobacillus minor NM305] ref|ZP_03800364.1| hypothetical protein 37.24 145 83 4 16226 16636 COPCOM_02633 [Coprococcus comes ATCC 27758] ref|ZP_01791611.1| hypothetical protein 37.18 156 98 2 21169 20702 CGSHiAA_00570 [Haemophilus influenzae PittAA] ref|YP_864938.1| hypothetical protein 28.05 353 202 14 27287 26385 Mmc1_1014 [Magnetococcus sp. MC-1] ref|ZP_02327247.1| DNA/RNA helicase 27.17 254 182 8 12324 13076 [Paenibacillus larvae subsp. larvae BRL- 230010] ref|ZP_02327247.1| DNA/RNA helicase 26.73 101 73 2 11996 12295 [Paenibacillus larvae subsp. larvae BRL- 230010] ref|ZP_06223211.1| hypothetical protein 38.16 152 94 2 21157 20702 HAINFHK1212_0035 [Haemophilus influenzae HK1212] gb|ACD75432.1| AMDV4_3 29.43 265 163 8 15941 16663 [uncultured virus] ref|YP_002276802.1| Tail Collar domain 31.25 240 149 8 22027 21356 protein [Gluconacetobacter diazotrophicus PAl 5] gb|ADD81106.1| TerL [Rhodococcus 30.66 212 143 6 1378 755 phage ReqiPine5] ref|YP_002475454.1| hypothetical 34.15 164 108 2 21193 20702 bacteriophage protein [Haemophilus parasuis SH0165] ref|YP_002276931.1| Tail Collar domain 30.51 295 185 12 22180 21356 protein [Gluconacetobacter diazotrophicus PAl 5] ref|YP_001862243.1| hypothetical protein 34.57 162 106 4 21190 20705 Bphy_6144 [Burkholderia phymatum STM815] ref|ZP_05555322.1| conserved hypothetical 25.21 361 235 15 1450 473 protein [Lactobacillus crispatus MV-1A-US] ref|ZP_05377878.1| Pathogenesis-related 38.16 152 89 4 11490 11930 transcriptional factor and ERF protein ref|ZP_04601775.1| hypothetical protein 29.45 163 115 2 21193 20705 GCWU000324_01248 [Kingella oralis ATCC 51147] ref|ZP_01789655.1| hypothetical protein 34.34 166 109 2 21202 20705 CGSHi3655_00165 [Haemophilus influenzae 3655] ref|YP_239069.1| hypothetical protein 35.29 153 98 2 11517 11972 RB43ORF093w [Enterobacteria phage RB43] ref|ZP_05346792.1| DNA/RNA helicase 26.15 260 189 8 12306 13076 [Bryantella formatexigens DSM 14469] ref|ZP_05346792.1| DNA/RNA helicase 29.70 101 70 2 11996 12295 [Bryantella formatexigens DSM 14469] ref|YP_001850249.1| hypothetical protein 26.77 269 190 7 1561 776 MMAR_1945 [Mycobacterium marinum M] ref|YP_001850249.1| hypothetical protein 28.91 128 90 2 2722 2342 MMAR_1945 [Mycobacterium marinum M] ref|ZP_03009318.1| hypothetical protein 25.84 267 190 9 12297 13073 BACCOP_01174 [Bacteroides coprocola DSM 17136] ref|ZP_03009318.1| hypothetical protein 31.78 107 68 4 11996 12301 BACCOP_01174 [Bacteroides coprocola DSM 17136] ref|ZP_06342161.1| DEAD/DEAH box 26.82 261 187 8 12306 13076 helicase [Bulleidia extructa W1219] ref|ZP_06342161.1| DEAD/DEAH box 32.99 97 64 2 11996 12283 helicase [Bulleidia extructa W1219] ref|ZP_06646295.1| DNA/RNA helicase 27.60 221 158 6 12420 13076 [Erysipelotrichaceae bacterium 5_2_54FAA] ref|ZP_06646295.1| DNA/RNA helicase 30.00 110 76 3 11996 12322 [Erysipelotrichaceae bacterium 5_2_54FAA] ref|YP_398997.1| putative ATP- 24.37 435 293 14 12414 13610 dependent helicase [Enterobacteria phage RTP] ref|YP_363378.1| hypothetical protein 34.25 181 105 6 21193 20693 XCV1647 [Xanthomonas campestris pv. vesicatoria ref|ZP_02328732.1| DNA/RNA helicase 27.45 255 181 9 12324 13076 [Paenibacillus larvae subsp. larvae BRL- 230010] ref|ZP_02328732.1| DNA/RNA helicase 26.73 101 73 2 11996 12295 [Paenibacillus larvae subsp. larvae BRL- 230010] ref|ZP_06704951.1| conserved hypothetical 34.25 181 105 6 21193 20693 protein [Xanthomonas fuscans subsp. aurantifolii ref|NP_641937.1| hypothetical protein 34.25 181 105 6 21193 20693 XAC1605 [Xanthomonas axonopodis pv. citri str. ref|ZP_04566003.1| type III restriction 26.58 222 161 6 12417 13076 enzyme [Mollicutes bacterium D7] ref|ZP_04566003.1| type III restriction 31.37 102 69 2 11996 12298 enzyme [Mollicutes bacterium D7] ref|XP_002492528.1| Putative protein of 25.97 258 176 8 12327 13055 unknown function [Pichia pastoris GS115] ref|XP_002492528.1| Putative protein of 25.89 112 76 4 11996 12310 unknown function [Pichia pastoris GS115] ref|NP_705681.1| gp58 [Burkholderia 25.38 264 183 8 12327 13076 phage Bcep781] ref|NP_705681.1| gp58 [Burkholderia 30.97 113 71 3 11999 12316 phage Bcep781] ref|NP_858950.1| endonuclease of the 37.50 136 84 3 11475 11879 HNH family [Xanthomonas phage Xp10] ref|YP_001293436.1| hypothetical protein 26.37 292 205 9 12333 13178 ORF029 [Pseudomonas phage 73] ref|YP_001293436.1| hypothetical protein 32.41 108 69 3 11999 12310 ORF029 [Pseudomonas phage 73] ref|ZP_03385165.1| putative helicase 42.73 110 63 1 11996 12325 [Salmonella enterica subsp. enterica serovar Typhi ref|YP_001294897.1| helicase [Burkholderia 25.38 264 183 8 12327 13076 phage BcepNY3] ref|YP_001294897.1| helicase [Burkholderia 30.97 113 71 3 11999 12316 phage BcepNY3] ref|NP_958163.1| gp57 [Burkholderia 25.38 264 183 8 12327 13076 phage Bcep43] ref|NP_958163.1| gp57 [Burkholderia 30.97 113 71 3 11999 12316 phage Bcep43] ref|NP_944368.1| gp60 [Burkholderia 25.38 264 183 8 12327 13076 phage Bcep1] ref|NP_944368.1| gp60 [Burkholderia 30.97 113 71 3 11999 12316 phage Bcep1] ref|YP_164394.1| DEAD box family 25.78 256 187 7 12318 13076 helicase [Bacillus phage BCJA1c] ref|YP_164394.1| DEAD box family 25.69 109 80 2 11996 12319 helicase [Bacillus phage BCJA1c] ref|YP_002911934.1| P42.1 [Burkholderia 38.30 141 86 2 11496 11915 glumae BGR1] ref|NP_203468.1| hypothetical protein 29.24 342 216 12 27287 26340 Mx8p54 [Myxococcus phage Mx8] ref|ZP_04682609.1| p077 [Ochrobactrum 28.38 229 159 4 8671 9342 intermedium LMG 3301] ref|YP_003065546.1| hypothetical protein 35.46 141 84 2 27703 27302 CLIBASIA_05175 [Candidatus Liberibacter asiaticus ref|YP_239236.1| hypothetical protein 30.18 169 112 4 11463 11951 RB43ORF260w [Enterobacteria phage RB43] ref|ZP_06111909.1| ferrichrome transport 37.61 117 70 2 15944 16285 ATP-binding protein FhuC [Clostridium botulinum ref|ZP_05113457.1| hypothetical protein 43.75 96 54 1 3278 2991 SADFL11_1342 [Labrenzia alexandrii DFL-11] ref|ZP_03529250.1| hypothetical protein 31.51 146 100 1 37125 36688 RetlC8_22061 [Rhizobium etli CIAT 894] ref|ZP_05860237.1| DNA/RNA helicase 25.00 312 223 14 12327 13229 [Jonquetella anthropi E3_33 E1] ref|ZP_05860237.1| DNA/RNA helicase 35.71 112 69 5 11996 12322 [Jonquetella anthropi E3_33 E1] ref|YP_002564202.1| gp6 [Mycobacterium 33.98 206 130 8 1375 776 phage Phlyer] ref|YP_002564202.1| gp6 [Mycobacterium 25.00 132 85 3 2722 2369 phage Phlyer] ref|NP_945017.1| Putative HNH 35.22 159 99 4 11475 11939 endonuclease [Enterobacteria phage Felix 01] ref|ZP_01054763.1| putative DEAD box 26.95 308 195 12 12333 13166 family helicase, phage associated [Roseobacter sp. ref|ZP_01054763.1| putative DEAD box 33.33 84 54 3 11996 12241 family helicase, phage associated [Roseobacter sp. ref|ZP_05377955.1| Pathogenesis-related 33.55 152 99 3 11475 11924 transcriptional factor and ERF protein ref|YP_724333.1| hypothetical protein 31.36 169 114 5 21211 20711 Tery_4946 [Trichodesmium erythraeum IMS101] ref|YP_002014616.1| gp5 [Mycobacterium 33.98 206 130 8 1375 776 phage Phaedrus] ref|YP_002014616.1| gp5 [Mycobacterium 25.00 132 85 3 2722 2369 phage Phaedrus] ref|YP_003610365.1| protein of unknown 32.52 163 110 3 21193 20705 function DUF847 [Burkholderia sp. CCGE1002] ref|ZP_06222216.1| hypothetical protein 37.93 145 90 2 21136 20702 HAINFHK1212_0433 [Haemophilus influenzae HK1212] ref|ZP_06221530.1| hypothetical protein 37.93 145 90 2 21136 20702 HAINFHK1212_1001 [Haemophilus influenzae HK1212] ref|ZP_05988809.1| putative phage large 28.48 309 213 13 1378 476 subunit terminase [Mannheimia haemolytica ref|ZP_05988809.1| putative phage large 30.17 116 81 1 2737 2390 subunit terminase [Mannheimia haemolytica ref|ZP_05854350.1| DNA (cytosine-5-)- 28.24 255 168 6 15935 16654 methyltransferase [Blautia hansenii DSM 20583] ref|YP_785834.1| phage large subunit 29.36 327 219 14 1378 434 terminase [Bordetella avium 197N] ref|YP_785834.1| phage large subunit 29.41 119 83 2 2743 2390 terminase [Bordetella avium 197N] ref|ZP_01048606.1| phage uncharacterized 26.00 350 239 13 1462 473 protein [Nitrobacter sp. Nb-311A] ref|ZP_01048606.1| phage uncharacterized 26.89 119 86 1 2677 2324 protein [Nitrobacter sp. Nb-311A] ref|YP_655728.1| gp48 [Mycobacterium 25.79 221 160 4 12402 13052 phage Qyrzula] ref|YP_655728.1| gp48 [Mycobacterium 35.92 103 63 3 11996 12295 phage Qyrzula] ref|NP_817811.1| gp50 [Mycobacterium 25.79 221 160 4 12402 13052 phage Rosebush] ref|NP_817811.1| gp50 [Mycobacterium 35.92 103 63 3 11996 12295 phage Rosebush] ref|YP_003429878.1| putative DEAD box 24.71 259 186 7 12327 13076 family helicase, phage associated [Streptococcus ref|YP_003429878.1| putative DEAD box 30.39 102 70 2 11996 12298 family helicase, phage associated [Streptococcus ref|YP_001736109.1| hypothetical protein 29.15 319 220 12 12216 13154 SYNPCC7002_C0009 [Synechococcus sp. PCC 7002] ref|YP_001736109.1| hypothetical protein 30.59 85 58 3 11987 12238 SYNPCC7002_C0009 [Synechococcus sp. PCC 7002] ref|YP_002501630.1| phage uncharacterized 28.62 318 211 10 1378 473 protein [Methylobacterium nodulans ORS 2060] ref|YP_002501630.1| phage uncharacterized 31.73 104 65 3 2677 2384 protein [Methylobacterium nodulans ORS 2060] ref|YP_001834420.1| hypothetical protein 32.18 174 117 5 21190 20672 Bind_3374 [Beijerinckia indica subsp. indica ATCC ref|NP_597900.1| putative endonuclease 30.87 149 102 2 11472 11915 [Enterobacteria phage HK022] ref|YP_001950208.1| HNH endonuclease 31.82 176 107 5 11481 11969 [Ralstonia phage RSL1] ref|ZP_01724547.1| hypothetical protein 33.11 151 98 2 1378 935 BB14905_13950 [Bacillus sp. B14905] ref|ZP_01724547.1| hypothetical protein 33.87 124 80 3 2734 2369 BB14905_13950 [Bacillus sp. B14905] ref|YP_277511.1| hypothetical protein 31.90 232 141 7 12411 13055 yejH [Enterobacteria phage JK06] ref|YP_277511.1| hypothetical protein 29.46 112 77 2 12002 12331 yejH [Enterobacteria phage JK06] ref|NP_936907.1| hypothetical protein 30.81 172 115 2 21190 20687 VVA0851 [Vibrio vulnificus YJ016] ref|XP_001485376.1| hypothetical protein 29.92 264 170 10 12306 13052 PGUG_03105 [Pichia guilliermondii ATCC 6260] ref|XP_001485376.1| hypothetical protein 26.42 106 73 2 11996 12298 PGUG_03105 [Pichia guilliermondii ATCC 6260] ref|ZP_05377917.1| Pathogenesis-related 34.57 162 105 4 11490 11972 transcriptional factor and ERF protein ref|YP_002235510.1| putative 32.66 248 150 11 15944 16636 methyltransferase [Burkholderia cenocepacia J2315] ref|ZP_04996124.1| conserved hypothetical 36.36 132 84 4 1375 980 protein [Streptomyces sp. Mg1] ref|XP_001528318.1| hypothetical protein 32.70 263 167 10 12306 13064 LELG_00838 [Lodderomyces elongisporus NRRL ref|YP_676376.1| DNA methylase N- 26.38 254 183 4 15941 16690 4/N-6 [Mesorhizobium sp. BNC1] ref|YP_865217.1| type III restriction 25.94 293 203 9 12333 13169 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_865217.1| type III restriction 27.62 105 72 2 11993 12295 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_865981.1| type III restriction 25.00 296 205 9 12333 13169 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_865981.1| type III restriction 27.62 105 72 2 11993 12295 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_866555.1| type III restriction 25.17 286 197 8 12333 13139 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_866555.1| type III restriction 27.62 105 72 2 11993 12295 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_002922621.1| P07 [Xanthomonas 40.21 97 57 1 11610 11897 phage phiL7] ref|ZP_03588245.1| DNA methylase 31.51 238 156 8 15944 16636 [Burkholderia multivorans CGD1] ref|ZP_01983885.1| DNA methylase 28.24 262 160 9 15941 16642 [Vibrio cholerae 623-39] ref|ZP_06258255.1| DEAD/DEAH box 24.81 266 191 7 12306 13076 helicase [Veillonella parvula ATCC 17745] ref|ZP_06258255.1| DEAD/DEAH box 35.37 82 52 3 11996 12238 helicase [Veillonella parvula ATCC 17745] ref|ZP_06351481.1| DNA methylase N- 29.62 260 167 7 15914 16645 4/N-6 domain protein [Rhodomicrobium vannielii ATCC ref|ZP_06222326.1| hypothetical protein 37.76 143 89 2 21130 20702 HAINFHK1212_0129 [Haemophilus influenzae HK1212] ref|ZP_06221926.1| hypothetical protein 37.76 143 89 2 21130 20702 HAINFHK1212_0534 [Haemophilus influenzae HK1212] ref|YP_002498769.1| phage uncharacterized 25.87 317 220 10 1378 473 protein [Methylobacterium nodulans ORS 2060] ref|ZP_03521690.1| hypothetical protein 26.10 272 200 4 32466 31654 RetlG_10420 [Rhizobium etli GR56] ref|YP_001533100.1| hypothetical protein 34.27 178 93 5 21196 20735 Dshi_1757 [Dinoroseobacter shibae DFL 12] gb|EDK39007.2| hypothetical protein 29.55 264 171 10 12306 13052 PGUG_03105 [Pichia guilliermondii ATCC 6260] gb|EDK39007.2| hypothetical protein 26.42 106 73 2 11996 12298 PGUG_03105 [Pichia guilliermondii ATCC 6260] ref|ZP_06393533.1| protein of unknown 32.61 184 110 5 21202 20693 function DUF847 [Dethiosulfovibrio peptidovorans DSM ref|ZP_03544066.1| phage uncharacterized 28.35 321 221 13 1378 443 protein [Comamonas testosteroni KF-1] ref|ZP_03544066.1| phage uncharacterized 27.35 117 84 2 2737 2390 protein [Comamonas testosteroni KF-1] ref|YP_001119034.1| hypothetical protein 30.06 163 114 3 21193 20705 Bcep1808_1188 [Burkholderia vietnamiensis G4] ref|YP_866744.1| type III restriction 25.68 296 203 10 12333 13169 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_866744.1| type III restriction 27.62 105 72 2 11993 12295 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_002898982.1| hypothetical protein 35.21 142 91 4 11475 11897 EE36P1_gp51 [Roseophage EE36P1] ref|ZP_01976970.1| ATP-dependent RNA 30.10 206 143 7 13041 13655 helicase, DEAD/DEAH box family [Vibrio cholerae B33] ref|YP_001899851.1| protein of unknown 29.45 163 115 3 21193 20705 function DUF847 [Ralstonia pickettii 12J] ref|ZP_06681838.1| gp10 [Enterococcus 28.07 171 117 4 15941 16435 faecium E980] ref|YP_001600402.1| putative DNA 27.54 236 167 3 15941 16636 methylase N-4/N-6 [Gluconacetobacter diazotrophicus PAl 5] ref|XP_001390242.1| hypothetical protein 26.07 257 182 7 12306 13052 An03g03600 [Aspergillus niger] ref|XP_001390242.1| hypothetical protein 28.21 78 54 2 11993 12220 An03g03600 [Aspergillus niger] gb|EFG84791.1| putative DNA 28.23 248 162 5 15941 16636 methylase N-4/N-6 [Gluconacetobacter hansenii ATCC 23769] ref|ZP_05843252.1| protein of unknown 34.50 171 88 5 21175 20735 function DUF847 [Rhodobacter sp. SW2] ref|YP_002274239.1| putative HNH 30.20 149 103 2 11472 11915 endonuclease [Stx2- converting phage 1717] ref|ZP_01034820.1| hypothetical protein 35.56 180 91 7 21175 20711 ROS217_23282 [Roseovarius sp. 217] ref|YP_840552.1| DNA methylase N- 30.74 283 179 12 15839 16636 4/N-6 domain- containing protein [Burkholderia ref|YP_002964945.1| HNH endonuclease 34.27 143 93 2 11490 11915 family protein [Methylobacterium extorquens AM1] ref|YP_001110809.1| hypothetical protein 34.55 165 103 5 11490 11969 SPSV3_gp09 [Salmonella phage SETP3] ref|YP_529251.1| XRE family 32.14 168 104 4 21169 20696 transcriptional regulator [Saccharophagus degradans 2-40] ref|ZP_06178203.1| conserved hypothetical 27.82 266 178 9 12321 13076 protein [Vibrio harveyi 1DA3] ref|ZP_06178203.1| conserved hypothetical 38.57 70 43 2 11993 12202 protein [Vibrio harveyi 1DA3] ref|ZP_06142710.1| type III restriction 26.75 228 159 7 12417 13076 protein res subunit [Ruminococcus flavefaciens ref|ZP_06142710.1| type III restriction 31.68 101 68 2 11996 12295 protein res subunit [Ruminococcus flavefaciens gb|EFG69405.1| DNA methylase N- 28.05 246 162 9 15947 16639 4/N-6 domain protein [Burkholderia sp. Ch1- 1] ref|ZP_06542003.1| putative helicase 52.63 95 43 1 12741 13019 [Salmonella enterica subsp. enterica serovar Typhi ref|YP_002502042.1| phage uncharacterized 27.86 323 225 12 1378 434 protein [Methylobacterium nodulans ORS 2060] ref|ZP_01948157.1| conserved hypothetical 30.23 172 116 2 21190 20687 protein [Vibrio cholerae 1587] ref|YP_655687.1| gp7 [Mycobacterium 30.77 208 136 7 1375 776 phage Qyrzula] ref|YP_655687.1| gp7 [Mycobacterium 25.56 133 84 3 2722 2369 phage Qyrzula] gb|AAY44387.1| RB16 HNH(AP2) 2 38.00 150 92 6 11493 11939 [Enterobacteria phage RB16] ref|NP_817768.1| gp7 [Mycobacterium 30.77 208 136 7 1375 776 phage Rosebush] ref|NP_817768.1| gp7 [Mycobacterium 26.32 133 83 3 2722 2369 phage Rosebush] ref|ZP_01040991.1| primase, putative 30.42 263 170 10 5942 6691 [Erythrobacter sp. NAP1] ref|ZP_02192066.1| type III restriction 28.33 293 195 11 12333 13166 enzyme, res subunit [alpha proteobacterium BAL199] ref|ZP_02192066.1| type III restriction 31.43 105 68 3 11993 12295 enzyme, res subunit [alpha proteobacterium BAL199] ref|ZP_03682448.1| hypothetical protein 24.05 262 194 9 12306 13076 CATMIT_01082 [Catenibacterium mitsuokai DSM 15897] ref|ZP_03682448.1| hypothetical protein 28.57 105 73 3 11996 12304 CATMIT_01082 [Catenibacterium mitsuokai DSM 15897] ref|ZP_01878875.1| hypothetical protein 35.50 169 85 5 21175 20741 RTM1035_05155 [Roseovarius sp. TM1035] gb|AAX12931.1| hypothetical protein 35.81 148 88 4 21190 20768 [Escherichia blattae DSM 4481] ref|YP_001121090.1| type III restriction 26.19 294 202 11 12333 13169 enzyme, res subunit [Burkholderia vietnamiensis ref|YP_001121090.1| type III restriction 29.25 106 75 1 11993 12310 enzyme, res subunit [Burkholderia vietnamiensis gb|EFG70468.1| protein of unknown 33.13 163 109 4 21193 20705 function DUF847 [Burkholderia sp. Ch1- 1] ref|ZP_06050227.1| secretion activator 30.81 172 115 2 21190 20687 protein [Vibrio cholerae CT 5369-93] ref|ZP_04683498.1| Hypothetical protein 34.84 155 99 4 21157 20699 OINT_3000003 [Ochrobactrum intermedium LMG 3301] ref|ZP_04417624.1| secretion activator 30.23 172 116 2 21190 20687 protein [Vibrio cholerae 12129(1)] ref|YP_001241623.1| putative phage tail 29.25 212 137 5 21946 21350 Collar domain [Bradyrhizobium sp. BTAi1] ref|ZP_01972132.1| conserved hypothetical 30.23 172 116 2 21190 20687 protein [Vibrio cholerae NCTC 8457] ref|YP_317463.1| DNA methylase N- 25.83 240 174 3 15929 16636 4/N-6 [Nitrobacter winogradskyi Nb-255] ref|ZP_01075891.1| hypothetical protein 32.68 153 103 2 21163 20705 MED121_02105 [Marinomonas sp. MED121] ref|ZP_04629946.1| hypothetical protein 32.19 146 98 3 11490 11924 yberc0001_14950 [Yersinia bercovieri ATCC 43970] ref|YP_866508.1| type III restriction 27.86 280 187 10 12375 13169 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_866508.1| type III restriction 25.74 101 75 1 11993 12295 enzyme, res subunit [Magnetococcus sp. MC-1] ref|YP_001371723.1| DNA methylase N- 25.85 236 171 3 15941 16636 4/N-6 domain- containing protein [Ochrobactrum anthropi ref|YP_282807.1| adenine-specific 30.40 250 152 11 15953 16636 methyltransferase [Streptococcus pyogenes MGAS5005] ref|NP_437108.1| hypothetical protein 50.00 76 38 0 21049 20822 SM_b20828 [Sinorhizobium meliloti 1021] ref|YP_917737.1| hypothetical protein 36.31 168 83 5 21172 20741 Pden_3975 [Paracoccus denitrificans PD1222] ref|XP_002148691.1| DEAD/DEAH box 24.80 250 180 8 12327 13052 helicase, putative [Penicillium marneffei ATCC 18224] ref|XP_002148691.1| DEAD/DEAH box 32.53 83 54 2 11978 12220 helicase, putative [Penicillium marneffei ATCC 18224] ref|ZP_06079511.1| secretion activator 30.23 172 116 2 21190 20687 protein [Vibrio sp. RC586] ref|ZP_03587372.1| EF hand domain 28.90 173 111 6 21190 20708 protein [Burkholderia multivorans CGD1] ref|ZP_03274694.1| protein of unknown 29.55 220 141 10 21199 20582 function DUF847 [Arthrospira maxima CS-328] ref|ZP_02139834.1| hypothetical protein 28.48 323 210 13 1378 473 RLO149_03017 [Roseobacter litoralis Och 149] ref|ZP_02139834.1| hypothetical protein 30.09 113 78 1 2677 2342 RLO149_03017 [Roseobacter litoralis Och 149] ref|YP_001045164.1| DNA methylase N- 28.57 266 173 7 15926 16672 4/N-6 domain- containing protein [Rhodobacter ref|ZP_01955098.1| conserved hypothetical 30.23 172 116 2 21190 20687 protein [Vibrio cholerae MZO-3]

As mentioned herein above, the present invention also contemplates isolated polynucleotides which hybridize to the isolated polynucleotides described herein above. Such polynucleotides may be used to monitor Brucella phage gene expression, eventually allowing detection of Brucella strains (i.e. diagnosing) in a bacterial contaminated environment.

Such polynucleotides typically comprises a region of complementary nucleotide sequence that hybridizes under experimental conditions to at least about 8, 10, 13, 15, 18, 20, 22, 25, 30, 40, 50, 55, 60, 65, 70, 80, 90, 100, 120 (or any other number in-between) or more consecutive nucleotides to the sequence of the Brucella phage.

The polynucleotide (or plurality thereof) may be fixed to a solid support (e.g. in an array) and may be used to monitor phage expression in a Brucella sample.

Alternatively, the polynucleotide may serve as a primer in a primer pair and may be used in an amplification reaction (e.g. PCR) to identify Brucella phage.

The conditions are selected such that hybridization of the polynucleotide to the Brucella phage sequence is favored and hybridization to other non Brucella phage nucleic acid sequences is minimized.

By way of example, hybridization of short nucleic acids (below 200 bp in length, e.g. 13-50 bp in length) can be effected by the following hybridization protocols depending on the desired stringency; (i) hybridization solution of 6×SSC and 1% SDS or 3 M TMACl, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 μg/ml denatured salmon sperm DNA and 0.1% nonfat dried milk, hybridization temperature of 1-1.5° C. below the Tm, final wash solution of 3 M TMACl, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS at 1-1.5° C. below the Tm (stringent hybridization conditions) (ii) hybridization solution of 6×SSC and 0.1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 μg/ml denatured salmon sperm DNA and 0.1% nonfat dried milk, hybridization temperature of 2-2.5° C. below the Tm, final wash solution of 3 M TMACl, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS at 1-1.5° C. below the Tm, final wash solution of 6×SSC, and final wash at 22° C. (stringent to moderate hybridization conditions); and (iii) hybridization solution of 6×SSC and 1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 μg/ml denatured salmon sperm DNA and 0.1% nonfat dried milk, hybridization temperature at 2.5-3° C. below the Tm and final wash solution of 6×SSC at 22° C. (moderate hybridization solution).

The polynucleotides may further be labeled with detectable moieties. Methods for labeling nucleic acid molecules are well-known in the art. For a review of labeling protocols, label detection techniques, and recent developments in the field, see, for example, L. J. Kricka, Ann. Clin. Biochem. 2002, 39: 114-129; R. P. van Gijlswijk et al., Expert Rev. Mol. Diagn. 2001, 1: 81-91; and S. Joos et al., J. Biotechnol. 1994, 35: 135-153.

As mentioned, the present inventors have identified a region within the Brucella phage genome which serves as a regulatory sequence in Brucella and other bacteria—see Table 3 of the Examples section herein below.

Thus, according to another aspect of the present invention there is provided a method of down-regulating expression of a gene of interest in bacteria, the method comprising transforming bacteria with a nucleic acid construct which comprises a Brucella phage regulatory sequence, thereby down-regulating expression of the gene of interest.

The phrase “Brucella bacteria” as used herein, refers to all strains of Brucella including, but not limited to B. abortus strain 544, B. Suis strain 1330 and B. melitensis strain 16M. According to a particular embodiment, the downregulating is effected in the B. Suis strain or the B. melitensis of Brucella.

Examples of bacterial constructs include the pET series of E. coli expression vectors [Studier et al. (1990) Methods in Enzymol. 185:60-89). An example of a bacterial construct which allows expression in Brucella bacteria is the plasmid pBBR1mcs-4 (Kovach et al., 1995, Gene 1995; 166: 175-176), the contents of which are incorporated herein by reference and the pNSGroE plasmid (Seleem et al., BioTechniques 37:740-744 (November 2004), the contents of which are incorporated by reference herein.

It will be appreciated that the method of this aspect of the present invention may be used to down-regulate expression of a gene which is endogenous to the bacteria or endogenous to a phage which is comprised in the bacteria.

The gene of interest is preferably downregulated by at least 10%. According to one embodiment, the gene of interest is downregulated by about 50%. According to another embodiment, the gene of interest is downregulated by about 90%.

Examples of genes of interest include genes that encode polypeptides important for survival of the bacteria. By down-regulating such genes, the method may be used to kill the brucella bacteria, thereby treating a brucella infection.

The present invention contemplates insertion of transposon sequences on either side of the regulatory region such that it can be randomly inserted via a transposition event into the bacterial genome or site specific designed mutation.

As used herein, the term “transposition event” refers to the movement of a transposon from a donor site to a target site.

As used herein, the term “transposon” refers to a genetic element, including but not limited to segments of DNA or RNA that can move from one chromosomal site to another.

An exemplary transposon sequence is provided in SEQ ID NO: 398 (ME1 transposon sequence) and SEQ ID NO: 399 (ME2 transposon sequence). For directed down-regulation of a particular gene, bacterial sequences may be added on either side of the regulatory region, to facilitate a recombination event.

According to one embodiment, the regulatory region comprises from 100 to all the nucleotides of the nucleic acid sequence as set forth in SEQ ID NO: 396 (19630-18579).

Optionally, the nucleic acid construct comprises additional regulatory regions such as the one set forth in SEQ ID NO: 397 (16509-15500).

According to a particular embodiment, the nucleic acid construct further comprises a heterologous nucleic acid sequence and upstream thereto, a promoter sequence which directs expression of the heterologous nucleic acid sequence. The promoter sequence is selected such that it allows transcription of the heterologous nucleic acid sequence in the bacteria. Thus an exemplary promoter that may be used in Brucella is one set forth in SEQ ID NO: 400. Another promoter that may be used to express a heterologous nucleic acid sequence in Brucella include the groE promoter [Saleem et al., BioTechniques 37:740-744 (November 2004)]. Additional prokayotic promoters are also contemplated by the present inventors which are known in the art.

The regulatory region (for example SEQ ID NO: 396) is typically placed immediately downstream to the heterologous sequence in order to down-regulate expression thereof.

An exemplary construct contemplated by the present invention that may be used to show that SEQ ID NO: 396 comprises regulatory activity may comprise as follows:

i. a polynucleotide encoding a gene of interest (e.g. detectable moiety) operationally fused to a Brucella promoter; and

ii. a Brucella phage sequence fused to a 3′ end of the gene of interest, the regulatory sequence comprising from 100 nucleotides to all the nucleotides of the nucleic acid sequence as set forth in SEQ ID NO: 396.

Optionally, the construct may also comprise:

iii. a Brucella phage sequence fused to a 5′ end of the promoter, the sequence comprising from 100 nucleotides to all the nucleotides of the nucleic acid sequence as set forth in SEQ ID NO: 397.

It will be appreciated that when the heterologous nucleic acid sequence encodes a detectable moiety, it may be used to determine a strain of Brucella. The present inventors have shown that a plasmid construct comprising SEQ ID NO:396 placed immediately downstream of a detectable moiety can downregulate its expression in a strain specific manner. Thus, expression of the detectable moiety was almost completely down-regulated in B. suis and only partially down-regulated in B. melitensis. Such a construct can also be used to determine which bacteria are sensitive to the brucella phage regulatory region and engineer these bacteria by gene down-regulation. In addition, the construct may be used as a tool to decipher novel factors that modify promoter activity by analysis of the detectable signal.

The detectable moiety is typically comprised in a reporter polypeptide which emits a detectable signal. It may be a fluorescent signal (e.g. green fluorescent protein (GFP) red fluorescent protein (RFP) or yellow fluorescent protein (YFP)); a luminescent signal (e.g. luciferase—LUX) or a color signal (e.g. β-glucuronidase (GUS) and β.-galactosidase). In addition, transcribed RNAs of the polypeptides can be used as reporter products of the system.

According to a specific embodiment of this aspect of the present invention, the heterologous nucleic acid sequence encodes a LUX operon. Such an operon is encoded by the sequence as set forth in SEQ ID NO: 401. Further information regarding LUX operons may be found in Winson M K, Swift S, Hill P J, Sims C M, Griesmayr G, Bycroft B W, Williams P, Stewart GSAB. 1998, Engineering the luxCDABE genes from Photorhabdus luminescens to provide a bioluminescent reporter for constitutive and promoter probe plasmids and mini-Tn5 constructs. FEMS Microbiol Letteres 163: 193-202; Craney A Hohenauer T, Xu Y, Navani N K, Li Y, Nodwell J. 2007. A synthetic luxCDABE gene cluster optimized for expression in high-GC bacteria. Nuc Acid Res 35: No. 6 e46, both of which are incorporated herein by reference.

The present inventors identified sequences in the Brucella phage genome which were devoid of open reading frames and generated constructs which facilitated insertion of genes of interest (for example, those encoding detectable moieties) into the Brucella phage at those positions, so as not to affect the vital life cycle of the phage.

Thus, according to yet another aspect of the present invention there is provided a nucleic acid construct comprising:

i. a polynucleotide encoding a gene of interest operationally fused to a Brucella promoter;

ii. a first Brucella phage sequence fused to a 5′ end of the promoter, the first sequence comprising from 100 nucleotides to all the nucleotides of the nucleic acid sequence as set forth in SEQ ID NO: 394; and

iii. a second Brucella phage sequence fused to a 3′ end of the gene of interest, the second sequence comprising from 100 nucleotides to all the nucleotides of the nucleic acid sequence as set forth in SEQ ID NO: 395.

Since the flanking sequences around the gene of interest (i.e. SEQ ID NO: 394 and SEQ ID NO: 395) are Brucella phage sequences, such a construct may be used to insert the gene of interest by recombination into the Brucella phage genome.

If a phage is required which may be used to identify Brucella bacteria (and diagnose an infection), the gene of interest may encode a detectable moiety. Detectable moieties are further described herein above.

If a phage is required which may be used to kill Brucella bacteria, the gene of interest may encode a polypeptide which is lethal to Brucella bacteria. Such polypeptides may include anti-bacterial toxins (bacteriocins) and the like. In addition, non-translated sequences may be used to down-regulate important bacterial functions and factors that affect these sequences could be exploited to control bacterial functions.

Examples 3 and 4 of the Example section herein below describe a method of generating Brucella bacteria which carry the phage as co-residence of recombinant strains. Such carrier Brucella clones provide a means of unlimited chances to achieve direct recombinantional events between harbored foreign DNA and Brucella phage.

It will be appreciated that the phage which identifies Brucella bacteria by outputting a detectable signal (or carrier Brucella clones comprising same) may be used to diagnose a Brucella infection in a subject.

According to this aspect of the present invention, the method of diagnosing comprises contacting a sample of the subject with the recombinant Brucella phage described herein above. Infection of the Brucella bacteria with the recombinant Brucella phage would result in an increase in expression of the detectable moiety, thereby providing a signal that the infection is due to Brucella bacteria. The subject is typically a mammalian subject, e.g. sheep, cows, goats and humans.

Typically, the sample which is analyzed is a cellular sample derived from blood, urine, faeces, uterine, fetus membranes and placental membranes and fluids, mammary glands, lymph nodes, granuloma, sperm, testes, brain, cardio and renal organs, Cerebrospinal fluid (CSF), milk, dairy products, of the subject. Environmental samples (soil, aerosols, water) are also contemplated.

The terms “comprises”, “comprising”, “includes”, “including”, “having” and their conjugates mean “including but not limited to”.

The term “consisting of” means “including and limited to”.

The term “consisting essentially of” means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.

Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases “ranging/ranges between” a first indicate number and a second indicate number and “ranging/ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.

As used herein the term “method” refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.

It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.

Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with the above descriptions illustrate some embodiments of the invention in a non limiting fashion.

Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Culture of Animal Cells—A Manual of Basic Technique” by Freshney, Wiley-Liss, N.Y. (1994), Third Edition; “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.

General Materials and Methods

Purification of Phage Iz₁ and Extracting Genome DNA:

Phage Iz₁ was consecutively propagated on Brucella abortus reference strain 544 by inoculating drops of a phage Iz₁ suspension at routine test dilution (RTD) concentration on tryptic soy agar plates on which a 0.1 ml aliquot of a B. abortus strain 544 suspension was spread. After overnight growth at 37° C. in 5% CO₂ atmosphere plaques were collected into tryptic soy broth and enumerated for further preparations of RTD suspensions used in phage typing of Brucella isolates.

The same procedure was applied in order to purify phage Iz₁ particles for DNA extractions. However, phage suspension was prepared in TMGS buffer and filtered twice, first through 0.45 μm and subsequently through 0.2 μm filters in order to achieve a non-Brucella contaminated phage suspension.

2 ml of phage suspensions were centrifuged per tube using Sorvall RC M100 ultracentrifugation (Du-Pont). Ultracentrifugation was carried out at 10° C., for 4 hours at 60,000 rpm and DNA was extracted from phage pellets using QIAamp DNA Mini Kit, according to manufacturer's instructions (Qiagen GmbH, Hilden, Germany).

Cloning Phage Iz₁ HindIII DNA Fragments—Construction of Phage Iz1 HindIII Fragment Clones in E. coli Plasmid pBluescript:

Phage Iz₁ DNA was digested by HindIII, according to manufacturer's instructions (Fermentas Inc., Maryland, USA). The HindIII digestion profile concurred with previously published data (Rigby et al., Can J Vet Res. 1989; 53: 319-325). The DNA fragments were purified from agarose gel using Wizard® SV Gel system (Promega). Plasmid pBlueScript was digested by HindIII and purified from agarose gel using Wizard® SV Gel system (Promega). The purified pBlueScript plasmid and Phage Iz₁ DNA fragments were mixed, ligated and transformed to E. coli JM109 (Promega). Plasmid DNAs were extracted using HiYield Plasmid Mini Kit (RBC Bioscience, Taipei County, Taiwan).

DNA-DNA Hybridizations:

Hybridization was executed using DIG nonradioactive nucleic acid labeling and detection system, according to manufacturer's instructions (Roche Diagnostics GmbH, Mannheim, Germany).

Construction of Plasmid pBBR1mcs-43-II1053Lux_(CDABE):

Plasmid pBBR1mcs-41-II1053Lux_(CDABE) was constructed by inserting the Photorhabdus luminescens luxCDABE operon (Winson et al., 1998, FEMS Microbiol Letters 1998; 163: 193-202, incorporated herein by reference) into plasmid pBBR1mcs-4 (Kovach et al., 1995, Gene 1995; 166: 175-176).

Construction of Plasmids pBBR1mcs-4.1-II1053Lux_(CDABE) (15B-18B and 15A-18A, Respectively)

Specific Phage Iz₁ sequences were used as scaffold of the plasmid constructs. Primers were designed to include both Tn5 mosaic ends, 1 and 2, respectively. The KpnI::PstI sequence was added 5′ and PvuII::ME-1::KpnI sequence added to the 3′ end of fragment 15500 to 16509 of Phage Iz₁ amplicon. The SacI::ME-2::PvuII sequence was added 5′ and SalI::SacI added 3′ to 18579 to 19630 fragment of Phage Iz₁ amplicon (PvuII, KpnI, SacI, SalI are nucleotide sequences of the restriction endonuclease restriction sites of these enzymes; The position of the primers used to generate these constructs is illustrated in FIG. 4.

Phage Iz₁ naked DNA was used as the substrate in separate PCR DNA amplification reactions to obtain the desired amplicons. The first fragment [SacI::ME-2::PvuII-Iz(18579-19630)-SalI::SacI] was digested with SacI then ligated into a SacI linerized plasmid pBBR1mcs-4.1-II1053Lux_(CDABE) to generate an intermediate plasmid pBBR1mcs-4.1-II1053Lux_(CDABE)::SacI::ME-2::PvuII-Iz(18579-19630)-SalI::SacI, in orientations A and B (FIG. 3B). These plasmids were then used to construct the two complete plasmid structures shown in FIG. 3B by KpnI linearization of these constructs and ligation with fragment [KpnI::PstI-Iz(15500-16509)-PvuII::ME-1::KpnI] that established the two complete constructs shown in FIG. 3B. Importantly, Plasmid 15A-18A establishes an intact Tn5 transposon construct that includes Phage Iz₁ genome sequences flanking pLux. In contrast, plasmid 15B-18B includes pLux as an intact Tn5 transposon and phage Iz₁ sequences correctly orientated in the flanking ends of the intact Tn5::pLux construct.

Establishing Phage Iz₁ Pre-Infected-Electro-Competent Brucella suis Strain 1330 Cells:

Brucella suis strain 1330 was grown at 37° C. in 5% CO₂ atmosphere for 2 days on Trypticase soy agar supplemented with Serum-dextrose (Alton G G, Jones L M, Angus R D, Verger J M. Techniques for the brucellosis laboratory. Institute National de la Recherche Agronomique, Paris. 1988). Cells were collected by a plating loop and transferred to 6 ml Tryptic soy broth (TSB) establishing cell suspension at a concentration of around 10⁷-10⁸ cells/ml. Then, 1 ml of the cell suspension was inoculated into 22 ml of TSB in a 250 ml Erlenmeyer vessel and laid down to chill in the refrigerator for 2 hours. In total, 4 such Brucella suis strain 1330 cell suspensions were prepared. Incubation was stopped by taking each vessel out from the incubator to ambient temperature and 1 ml phage Iz₁ in TSB at ×10⁴ concentration of the routine test dilution (RTD, Alton et al., 1988) were added to the Brucella cell suspension. Taken that Brucella complete a single cycle of cells replication by 4 hours Brucella phage infection was allowed to a minimal period of 2 hours by incubating the cell suspension at 37° C. in 5% CO₂ atmosphere and chilling the cell suspension immediately after by incubation in ice. Then, the 4 cell suspensions were centrifuged for 13 minutes at 6500 rpm, in a fixed angle rotor at 4° C., each in a separate tube. The supernatants were spilled and every two cell pellets were pooled together and resuspended in 12 ml of 10% glycerol solution in double distilled water pre-cooled to 4° C. Washing in the cold (including pre-cooled pipettes and micro-tips) was repeated 4 times, each carried out by resuspending the pellet and repeated centrifugation for 13 minutes at 8000 rpm. The two cell pellets were resuspended and pooled together in 3 ml 10% glycerol and spun down at 8000 rpm for 10 minutes, at 4° C. The final cell pellet was then resuspended in 0.5 ml of pre-cooled 10% glycerol solution and further divided to aliquots of 50 μl each in pre-cooled eppendorf tubes that were immediately cooled to freezing using liquid nitrogen and then stored at −80° C. until use.

Example 1 Deciphering the Complete Phage Iz₁ Genome Sequence

Results

The complete genome sequence of phage Iz₁ has been deciphered using 454 Life Sciences™ Roche GS-FLX sequencing platform (DYN Labs, LTD, Israel). The largest contig that was identified includes 38,254 bp (SEQ ID NO: 1 and SEQ ID NO: 2). Within this contig, the present data identified two Brucella phage Iz₁ genome populations differing by an SNP or a heterozygote nucleotide (nucleotide 5546 was recorded as N but in fact it was conclusively identified as C, and the polymorphism was distributed equally in 8 contigs between C or A at nucleotide 5549, respectively (FIG. 1).

To further corroborate the sequence of the phage, 8 HindIII DNA digest segments (1.1, 2.1; 3.1; 4.1, 5.1; 5.2; 5.3; 7.3) from phage Iz₁ were sub-cloned into plasmid pBS and sequenced corroborating the established sequences of identical overlapping fragments in phage Iz₁ genome. In concordance with these results, whole genomic naked DNA of phage Iz₁ hybridized with each of these clones. Two additional clones, e.g., 5.4 and 71_(—)3 and 71_(—)5_I, included partial sequencing (FIG. 2).

The sequence of the phage was analyzed using BLAST ((Basic Local Alignment Search Tool) software.

The results are displayed in Table 2, herein below.

TABLE 2 Align- Query % ment Mis- gap q. q. id Description identity length matches openings start end contig 1 Ochrobactrum  91.64 299 25 0 19140 19438 anthropi ATCC 49188 chromosome 1, complete sequence contig 1 Ochrobactrum 100.00  46  0 0 17964 18009 anthropi ATCC 49188 chromosome 1, complete sequence contig 1 Ochrobactrum  97.62  42  1 0 17519 17560 anthropi ATCC 49188 chromosome 1, complete sequence contig 1 Ochrobactrum 100.00  37  0 0 16687 16723 anthropi ATCC 49188 chromosome 1, complete sequence contig 1 Ochrobactrum 100.00  35  0 0 17850 17884 anthropi ATCC 49188 chromosome 1, complete sequence contig 1 Ochrobactrum  93.33  45  1 2 17267 17310 anthropi ATCC 49188 chromosome 1, complete sequence

Results from the analysis of CpG islands show that although the observed/expected ratio>0.60, the actual percent C+percent G>50.00, indicating that the phage comprises sequences other than Brucella.

An inverted repeat was found at positions 5088-5179 and 5405-5310 suggesting a putative site of the origin of replication.

Using an internet based promoter finding tool (worldwidewebdotfruitflydotorg/seq_tools/promoter) the present inventors identified 183 potential promoters on the forward strand and 201 potential promoters on the reverse strand. The sequences of these promoters are set forth in SEQ ID NOs: 3-185 for the forward strand and 186-386 for the reverse strand.

Example 2 Regulating Brucella Genes by Phage Iz₁ Sequences

Plasmid constructs that include selected sequences from Phage Iz₁ genome were designed and transformed to E. coli JM109 including those indicated in FIG. 3B and Table 3, herein below. The plasmid constructs were then transformed to E. coli S17, as this strain supports plasmid transfer to Brucella by conjugation, and selecting Brucella clones by growth on ampicilin. Trans-conjugant Brucella strains with these constructs endowed specific clones with Lux activities that depended on the Phage Iz₁ inserts and the specific Brucella strain that was transformed with these plasmids. B. suis reference strain 1330, B. melitensis type strain 16M and B. abortus reference strain 544 have shown similar strong constitutive Lux expression, based on the promoter upstream of the Lux operon, when harboring plasmid pBBR1mcs4.1 II1053Lux_(CDABE)/15B-18B (see FIG. 3B). In contrast, plasmid pBBR1mcs4.1 II1053Lux_(CDABE)/15A-18A was lethal to B. abortus strain 544 (it was impossible to establish trans-conjugant clones with this construct even if ampicillin was reduced to 25 μg/ml, that is one forth of the normal selective concentration used with B. suis strain 1330). The same applied less severely to B. melitensis strain 16M that was selected on agar plates with ampicillin at concentration of 50 μg/ml. Only B. suis strain 1330 was successfully transformed with the plasmid construct using ampicillin at a concentration of 100 μg/ml. This proves that the Phage Iz₁ sequences conferred different lethal activities on Brucella species as the same plasmid that does not contain phage sequences could be successfully transformed to each of these Brucella strains.

Further, light activity was completely silenced in B. suis strain 1330 whereas it was partially expressed in B. melitensis strain 16M (Results could not be shown with B. abortus as the plasmid was lethal to this strain, as explained above). When arguing for silencing activities by Phage Iz₁ sequences this could be demonstrated by adding external n-decanal to Brucella suspensions. The pentacistronic Lux operon consists of a luxAB component that encodes for a bacterial luciferase that oxidizes FMNH₂ and a long-chain aliphatic aldehyde (n-decanal substrate) in the presence of molecular oxygen to yield a 490-nm optical signature. The aldehyde is subsequently regenerated by a multi-enzyme reductase complex encoded by the luxC, luxD, and luxE genes. Accordingly, the Lux operon is encoding two separate functions, expression of luciferase by genes A and B and the substrate, by genes, C, D and E, respectively. External N-decanal could be used as a substitute for the native substrate. Because the addition of external n-decanal to the cell suspension fully restored light in both B. suis strain 1330 pBBRImcs4.1 II1053Lux_(CDABE)/15A-18A and B. melitensis strain 16M pBBRImcs4.1 II1053Lux_(CDABE)/15A-18A, this indicates that luciferase was present in the reaction mixture at the time, inferring it was fully expressed under the promoter that resides upstream to Phage Iz1 15A and LuxC and Lux D, sequences. It is most likely therefore that gene LuxE, downstream of LuxA and LuxB was under unique regulation from Phage Iz₁ 18A sequence under the 3′ orientation. This is further supported by the fact that this regulation was exerted at different intensities between B. suis strain 1330 (null Lux activity) and B. melitensis strain 16M (partial Lux activity). As phage Iz₁ fully lyses B. abortus and B. suis strains but has only partial lysis on B. melitensis strains, our data corroborate the historical Brucella species phage typing method and support our invention that the 18A Phage Iz₁ sequence regulates Brucella gene expression.

Table 3, herein below provides additional plasmids comprising phage Iz1 sequences that are capable of down-regulating genes placed immediately downstream thereto in both brucella and other bacteria.

TABLE 3 Bacterial Max strain Plasmid luminescence Comments E. coli pBBR1mcs-4.1- 187000 RLU Lux was S17 II1053Lux_(CDABE) affected by strain physiology B. suis pBBR1mcs-4.1- Variable, up Lux was 1330 II1053Lux_(CDABE) to 1.5 × 10⁶ affected by RLU strain physiology B. melitensis pBBR1mcs-4.1- 7 × 10⁶ RLU Plasmid Elberg II1053Lux_(CDABE) was Rev. 1 maintained vaccine even under strain no antibiotic selection for several passages E. coli pBBR1mcs-4.1- 77 RLU Background JM109 II1053Lux_(CDABE)/18A level E. coli pBBR1mcs-4.1- Variable, up JM109 II1053Lux_(CDABE)/18B 21000 RLU B. suis pBBR1mcs-4.1- Variable, up By adding Susceptible 1330 II1053Lux_(CDABE)/18A to 3800 RLU external n- to phage Iz₁ decanal an over-load RLU was measured E. coli pBBR1mcs-4.1- 160 RLU By adding JM109 II1053Lux_(CDABE)/15A- external n- 18A decanal = 160000 RLU E. coli pBBR1mcs-4.1- 50000 RLU By adding JM109 II1053Lux_(CDABE)/15B- external n- 18B decal = 482000 RLU E. coli pBBR1mcs-4.1- 80 By adding S17 II1053Lux_(CDABE)/15A- external n- 18A decanal = 149000 RLU E. coli pBBR1mcs-4.1- 12000 RLU By adding S17 II1053Lux_(CDABE)/15B- external n- 18B decanal = 195000 RLU B. suis pBBR1mcs-4.1- Variable, up Similar 1330 II1053Lux_(CDABE)/15B- to 20 × 10⁶ representative 18B RLU results with two clones, 1; 3 B. suis pBBR1mcs-4.1- 217 RLU By adding Similar 1330 II1053Lux_(CDABE)/15A- external n- representative 18A decanal = results with up to two clones, 8.7 × 10⁶ 23; 32 RLU B. melitensis pBBR1mcs-4.1- 58000 RLU Clone 16 16M II1053Lux_(CDABE)/15A- 18A/ B. melitensis pBBR1mcs-4.1- 18 × 10⁶ RLU Clone 18 16M II1053Lux_(CDABE)/15B- 18B B. abortus pBBR1mcs-4.1- 1-3 × 10⁶ RLU Similar 2308 II1053Lux_(CDABE)/15B- representative 18B results with three clones, 4; 5; 10

pII1053 is strongly expressed in a constitutive manner in the three Brucella species, B. suis, B. melitensis and B. abortus. This promoter is expressed less intensively in E. coli.

The construct 18A downregulates Lux expression in both E. coli and Brucella, most likely by silencing LuxE.

Example 3 Establishing Phage Iz₁ Pre-Infected-Electro-Competent Brucella suis Strain 1330 Cells

In this example, the goal was to develop a method that will extend existence of phage Iz₁ infection of Brucella to an un-limited period of time in order to enable phage genome engineering at that time by recombinant DNA technology.

Naked phage DNA exists within bacterial cytosol immediately after phage infection following intrusion of the bacterial envelop by the phage DNA. Phage replication further ensues due to controlling bacterial gene expression and gearing the bacterial DNA replication machinery to a phage system. Prevention of DNA packaging into intact phage particles will therefore allow gene engineering of the phage genome by electroporation of the bacterial host during this period with recombinant DNA constructs that facilitate gene transposition or gene recombination. Accordingly, the present inventors hypothesized that phage infection could be arrested by chilling the Brucella host cells immediately after infection, then washing the Brucella cells several times using water-glycerol and freezing the cells at −80° C. until needed for electroporation.

Results

One eppendorf tube that contained phage arrested infection as described above, was taken out from the −80° C. freezer, and the cells were thawed on ice, and diluted to 1 ml by adding 0.95 ml of SOC-B solution (Lai F, Microb Pathog 1990; 9:363-368). Then, 1:10 dilutions of the cell suspension were prepared in cold physiological saline solution, up to 10⁻⁷. Drops of 10 μl were then inoculated on B. abortus strain 544 that was spread (0.1 ml of a TSB heavy cell suspension) on a TSA plate by a bacterial Drigalski spreader.

For comparison, an aliquot of the SOC-B cell suspension was passed through 0.45 μm syringe filter in order to ascertain that free Iz₁ phage particles did not exist in the cell suspension. The filtrate was similarly diluted 1:10 in physiological saline solution and 10 μl drops from each dilution were inoculated on B. abortus strain 544 plate (see above).

The two plates were incubated over night at 37° C. in 5% CO₂ atmosphere. The next day, plaques were sought in each dilution of whole cell suspension and cell-filtrate. The last dilution of the cell filtrate that yielded phage plaques was 10⁻² in which only two plaques were identified. In agreement with the dilution around 200 plaques were identified at 10⁻¹ dilution, indicating a minimal presence of free phage particles in the whole cell suspension prior to filtration. In contrast, the last dilution that yielded phage plaques by the whole cell suspension was 10⁻⁶, at which a single plaque was identified. In agreement with the dilutions, 10 plaques were identified at dilution 10⁻⁵ and concentrated plaques were found at 10⁻⁴ and below, indicating existence of close to a 4 logarithmic higher magnitude of phage particles in the cell suspension compared to the cell filtrate. All together, these data support the working hypothesis that despite interfering with phage replication by cooling off the cell suspension, cold washings and freezing at −80° C., the phage infection was fully restored when the cells were thawed and re-cultured. Similar results were achieved when phage infection was stopped after 1 hour and 15 minutes.

Example 4 Development of a Brucella Reporter Clone

The present example describes how a pre-phage infection state could be used to develop a recombinant phage Iz₁ clone that induces Lux activity in Brucella species. Such a recombinant clone could be used as a highly sensitive reporter to indicate presence of living Brucella cells in a suspected sample by light measurements in a host, its tissues (such as aborted placenta and fetus membranes and fluids) or milk samples.

Method

The method involves two steps (See FIG. 5). Firstly, a hybrid DNA was established between phage Iz₁ genomic DNA and plasmid pBBR1mcs4.1-II1053Lux_(CDABE)/15B-18B. Then, this hybrid DNA was electroporated to electrocompetent phage Iz₁ pre-infected B. suis strain 1330 cells and the cells were selected for ampicillin resistance. Phage Iz₁ carrier clones were identified amongst the growing colonies.

1. Establishing Hybrid DNA

A short denaturation and annealing process between equal amounts of phage Iz₁ and plasmid pBBR1mcs4.1-II1053Lux_(CDABE)/15B-18B DNAs was applied, the latter shares homologous sequences with the phage genome (FIGS. 3A-B). The final annealing step was stopped by bringing the reaction to 4° C., in order to establish hybrid DNA molecules between hybridizing single stranded DNAs of the two entities.

DNA denaturation and annealing was carried out in total volume of 25 μl reaction mixture using Biometra, T-Gradient, thermocycler, Germany. The thermocycling reactions were as follows:

Pre-heating: 95° C.-1.30′

6 cycles of: 95° C.-1.15′, 55.5° C.-2.00′, 72° C.-2.00′ Final annealing at 55.5° C.-7.00′

Stop at 4° C. 2. Electroporation

Electrocompetent pre-phage Iz₁ infected B. suis cells were used. 40 μl of electrocompetent cells were electroporated by adding 2 μl of the final thermocycling reaction mixture using bacterial mode of MicroPulser™, BIO-RAD, Hercules, Calif., USA (2.49 Kv, 4.9 ms). Immediately after electroporation, cells were suspended in 1 ml SOC-B (see above) and incubated with shaking at 37° C. for 1 hour and 30 min. A 1:10 dilution of the SOC-B electroporated cell suspension was prepared and 10 μl aliquots from both undiluted and 1:10 diluted SOC-B suspensions were inoculated on TSA plates that included 50 μg/ml ampicillin as the selecting antibiotic.

As a control, 10 μl drops of the electroporated cells in SOC-B and 1:10 dilution were inoculated on B. abortus strain 544 cells that were pre-spread on TSA agar plate in order to demonstrate phage Iz₁ infection of the electroporated B. suis strain 1330 cells.

Results

Non-electroporated cell suspension successfully grew on plain TSA plates but did not grow on TSA plates that included 50 μg/ml ampicillin. After electroporation, about 90 colonies grew on selective agar from the non-diluted SOC-B cell suspension and about 9 colonies grew from the 1:10 cell dilution. Four colonies from each dilution were selected for further analysis, each transferred on a TSA plate that included 50 μg/ml ampicillin. Table 4 herein below summarizes the luminescence and phage activity of electroporated clones.

TABLE 4 Clone No. Luminescence Phage activity 1 338,600 RLU + 2 943,500 RLU Neg 3 1.8 × 10⁶ RLU Neg 4 3.4 × 10⁶ RLU Neg 11 1.8 × 10⁶ RLU + 12 7.2 × 10⁶ RLU + 13 4.9 × 10⁶ RLU + 14 5.7 × 10⁶ RLU +

These results indicate the following: 1. Plasmid pBBR1mcs4.1-II1053Lux_(CDABE) was successfully transformed into these clones. 2. Smooth clones (2, 3, and 4) did not secret phage activity and rough clones were phage carriers (FIG. 5).

Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.

All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting. 

What is claimed is:
 1. An isolated polynucleotide comprising: (a) at least 100 consecutive nucleotides of the nucleic acid sequences selected from the group consisting of 387-393; (b) a heterologous nucleic acid sequence; and (c) a heterologous sequence which directs expression of said heterologous nucleic acid sequence, wherein said at least 100 consecutive nucleotides is positioned downstream to said (b) heterologous nucleic acid sequence.
 2. The isolated polynucleotide of claim 1 further comprising at least one nucleic acid sequence being selected from the group consisting of SEQ ID NO: 394 and 395 in a forward or reverse orientation.
 3. The isolated polynucleotide of claim 1, wherein said heterologous nucleic acid sequence encodes a detectable moiety.
 4. The isolated polynucleotide of claim 1, wherein said heterologous nucleic acid sequence encodes a polypeptide which is lethal to Brucella.
 5. A method of down-regulating expression of a gene of interest in a bacteria, the method comprising transforming bacteria with a nucleic acid construct which comprises the isolated polynucleotide of claim 1, thereby down-regulating expression of the gene of interest.
 6. The method of claim 4, wherein said bacteria comprises Brucella bacteria.
 7. The method of claim 6, wherein a strain of said Brucella bacteria comprises B. Suis or B. melitensis.
 8. The method of claim 5, wherein the gene is endogenous to the bacteria.
 9. The method of claim 5, wherein the gene is endogenous to a phage of the bacteria.
 10. The method of claim 5, wherein said regulatory sequence is flanked by a transposon sequence.
 11. A nucleic acid construct comprising the isolated polynucleotide of claim
 1. 12. The nucleic acid construct of claim 11, wherein said nucleic acid sequence is flanked by a transposon sequence.
 13. A nucleic acid construct comprising: i. a polynucleotide encoding a gene of interest operationally fused to a Brucella promoter; ii. a first Brucella phage sequence fused to a 5′ end of said promoter, said first sequence comprising at least 100 nucleotides of a nucleic acid sequence as set forth in SEQ ID NO: 394; and iii. a second Brucella phage sequence fused to a 3′ end of said gene of interest, said second sequence comprising at least 100 nucleotides of a nucleic acid sequence as set forth in SEQ ID NO:
 395. 14. The nucleic acid construct of claim 13, wherein said gene of interest encodes a therapeutic polypeptide.
 15. The nucleic acid construct of claim 13, wherein said gene of interest encodes a detectable moiety.
 16. A recombinant Brucella phage which identifies Brucella bacteria by outputting a detectable signal.
 17. The recombinant Brucella phage of claim 16 comprising lytic activity.
 18. An isolated Brucella bacterial cell comprising the recombinant Brucella phage of any of claims
 16. 19. A method of diagnosing a Brucella infection in a subject, the method comprising contacting a sample of the subject with the recombinant Brucella phage of claim 16, thereby diagnosing the Brucella infection.
 20. A method of diagnosing a Brucella infection in a subject, the method comprising contacting a sample of the subject with the isolated Brucella bacterial cell of claim 18, thereby diagnosing the Brucella infection. 